This is not intended as a replacement for the excellent VFAQ on the subject, nor the shop manuals, but is just a summary of the main tasks involved, and some of the little things that tend to not get documented in mainstream manuals. 
I strongly suggest following the pictures in the VFAQ while reading this description.
READ THE WHOLE THING BEFORE ATTEMPTING THIS. Actually, read this, the VFAQ, and the shop manual (or Haynes/Chiltons manual) procedure all the way through. Skimming all of these resources will result in you just having to read it in-depth while your transmission is hanging by a bolt and supported only by your knee and a stiff breeze.
First, you pretty much gut the passenger side of the engine bay. Disconnect the battery terminals, and remove the battery "box" (it's really just a plastic sheath over the battery) and battery from the car. There's a plastic tray underneath that just lifts out, and then there's a metal tray below that with four 12mm bolts that can be removed. There's a support frame underneath that which you might find handy to get out of your way; there are two 12mm bolts holding it to the passenger-side fender. Beneath that is a support holding some of your emissions equipment, assuming you still have yours. Remove the two 12mm bolts holding that support in place, and push the hoses and other such things out of your way.
Remove the air intake up to the turbo; this includes the flexible hose between the MAS and the turbo, the MAS itself, and the air box (in my case, a K&N filter; your configuration will probably differ). I just removed all three in a single piece; loosen the clamps on the turbo and blow-off valve dump tube, unbolt the K&N, and unplug the MAS, then lift the whole thing out in one easy piece. Don't forget about the two vacuum tubes on the back of the flexible intake pipe, and the one on the front (assuming yours are still connected). Push any vacuum hoses out of the way; the fat tube can be shoved out of the way, the tube from the valve cover can be removed completely to get it out of your hair, and the hose from the boost control solenoid below the MAS can be left hanging or removed (once again, assuming you still have any of these).
Disconnect your upper intercooler piping hose (the flexible piece between the upper intercooler pipe which holds your blow-off valve and the throttle body elbow). This may differ a bit, depending on your modifications; you may need to remove the entire upper intercooler piping setup, including blow-off valve, if you have a one-piece design. The basic idea is to expose the shifter cables.
Disconnect the shift and select cables. There are two cables that should be pretty well exposed at this point, with a small cotter pin holding each one down. The cotter pins will be pretty fragile, so be careful while straightening them. There should be a washer on each side of the cable end, try not to lose them. There are two 12mm bolts holding the cable bracket to the transaxle; remove them, and try to lift the cables out of your way. These will be in your way for the remainder of the procedure, unless you can successfully wedge them in somewhere; I didn't take my front strut bar off for this (it made for handy leverage a few times), so they were hard to reposition.
Remove the three bolts holding the clutch hydrolic line reservoir to the top of the transmission (look for a cylinder with hard lines coming in and out of it).
Disconnect the reverse light switch connector; this is a simple clip-on connector in plain sight near where the shift cables attached to the transaxle.
Disconnect the speedometer cable; this cable is located at the rear of the engine compartment, right beside the rear transaxle mount. You'll never actually see it, but there is a 10mm bolt beside the unit that the cable attaches to; run your finger down the side of the black tube that the cable attaches to (on the passenger side of it), and you'll feel the head of the bolt way down in there. Disconnect that bolt, and the entire unit will pull out (including a tall white gear at the end). When I removed the bolt, it slipped behind the engine; I didn't find it until the transmission came down. Note: I'm convinced that there must be a way to disconnect that cable without removing the speedometer cable gear, but it wasn't immediately obvious to me, and I had other things I wanted to get done at the time, so didn't get a chance to investigate further.
Remove the bolts between the transaxle and the engine. There are five 14mm bolts (three short ones, and two long ones at the front and the back, respectively), all reachable from above the car. LEAVE AT LEAST ONE BOLT IN PLACE. You don't want things coming apart early, although there's not much danger of that.
Remove the two 12mm bolts holding the starter in place. This is a bit of a pain in the neck; you might want to leave this step until after you've raised the car and removed the transfer case (see below) before doing this, as I found it damn near impossible to get at the starter from above.
Loosen the lugs on the passenger-side front wheel. Don't worry about the driver side, there's no reason you should need to remove that wheel during any of this.
Raise the vehicle. Be sure to place the jackstands behind any of the steering and suspension assembly, and raise the car as high as you can; you want enough room under the front of the car for both the transaxle and the jack (fully-lowered). Don't use the cheapo $10 jack you got from Wal-Mart; you can get the car in the air with it, and you can probably lower the transmission that way too, but you're going to hate getting the tranny back up there without a real floor jack and a transmission adapter. For reference, I picked up a 3-ton floor jack for about $95, and a transmission adapter kit (just a flat plate with some attachments for oddly-shaped items, and a post that goes where the usual round support plate goes) for about $50 at Farm and Fleet; I'm sure you could find a better deal if you shop around a bit.
Remove the front passenger-side wheel.
Disconnect the lower intercooler pipe (two clamps, one at the intercooler, one at the turbo). Remove the plastic under cover between the wheel and the transaxle (there's two or three 12mm bolts, if memory serves.
Drain the transaxle and the transfer case. See Brad Bauer's excellent explanation on how to do this.
Disconnect the bolts where your downpipe meets the O2 housing (or, if you have an O2-eliminating downpipe like me, disconnect the whole thing from the turbo). You don't strictly need to do this, but you definitely need to loosen things up so you have a little wiggle room (I didn't need to completely drop my downpipe, but I never would have reached all the bolts without some play in the piping). If you want to just remove the whole thing, there is a bolt on the downpipe ahead of the catalytic converter, and a couple of bolts holding it to the cat itself, as well as a grounding cable.
Go grab a wire hangar, open it up, and use it to create a good resting support for the rear driveshaft. Make sure it holds well; you don't want to drop the transfer case in the next step and have that joint land on the ground.
Remove the five 14mm bolts holding the transfer case to the transaxle. Three (one in front, two near the center) can be easily reached from below; the other two are positioned just above your downpipe, directly above the two on the bottom. This is where that downpipe wiggle room will come in handy. Once you have the bolts away from the transmission, use a screwdriver or small prybar to separate the transfer case from the transmission; it's not going to want to come away very easily. As you separate it, you'll see that there are a set of dowels around the edge holding it in place; they're a bit over a quarter-inch deep, to give you an idea of how far out you need to come. Careful, it can be a little heavy for a guy working on his back to catch when it separates; try and keep the rear raised, so you don't end up with transfer case fluid all over the place. Pull the transfer case toward the front of the car and off the driveshaft; it should separate easily. Make sure that you keep an eye on that driveshaft while you're pulling, to ensure that the wire hangar (or whatever you used) is holding securely.
Now for the most important step: Support the engine. We're going to start removing transaxle mounts soon, and of the four mounts holding your engine and transmission in the car, three of them are attached to the transmission. There are two approaches to this: either get a proper overhead support which gives you the most control over where you position everything, or be ghetto-fabulous. I chose door number two: a four-inch or so square piece of thin furniture plywood, with a few layers of padded rags on top of it, held in place right behind the oil supply line on the oil pan by a jack. Make sure this is extremely well-padded, and don't let anything bang against that oil tube!
Remove the gusset (a four-inch or so wide triangular structural member) and the long member running front to back on the passenger side (this differs from the VFAQ, which I suspect has an error; they mention the driver's side, but they have the passenger-side member pictured). There's about 9 bolts total, and some will be a royal pain to remove. Note that the front transaxle mount is attached to the member, so you'll either want to unbolt it from the transaxle now and take both down together, or disconnect it from the member, and remove it from the transaxle later.
Remove the 10mm bolt from the bottom of the flywheel inspection cover, which should be right in front of where the transfer case used to be. You could continue to remove the entire cover (two or three more bolts), but I didn't need to.
Remove the two 10mm (12mm?) bolts holding the clutch slave cylinder to the transmission bellhousing (there should be a hard line running from the clutch reservoir that you disconnected before to the slave cylinder, if you can't find it; you'll want to be under the front of the car for this).
Aim the steering wheel all the way left (ie. like you're turning left).
Remove the two bolts securing the lower control arm (the longish curved arm running from the wheel to the subframe just in front of the passenger-side door) to the subframe.
Remove the very large bolt on the frame side of the lateral control arm (the other, straight, arm coming from the wheel to the frame right beside the transmission). This bugger will take a little elbow grease to get out, and the VFAQ maintainer mentioned that his seized. Next, remove the bolt holding the other end of the later control arm to the wishbone/fork at the bottom of the strut.
Now for the driveshaft. There's no nice way to put it: this is a pain in the ass. You'll need a prybar; mine was a little shorter (about one and a half feet long) than I would have preferred, but it gave me plenty of clearance under the car to work with. I strongly suggest having a second person assist you with this; I was completely unsuccessful doing this by myself. You'll want to pry between the transaxle and the round green cylinder at the end of the driveshaft; while you pry (HARD) from below, have someone tap the green part from above (in my case, we tapped it from above with a breaker bar). The idea is to get a little vibration going to help settle the circlip at the end of the driveshaft in. You'll want to turn the shaft a little bit at a time as you go; once the orientation of the circlip is correct, the vibrations from the tapping to dislodge it and make the driveshaft pop right out. I spent hours on this just prying at it, and within five minutes of trying the tapping approach, the driveshaft came out. While you're prying, you might notice a rubber seal between the driveshaft and the transaxle; you will almost definitely destroy it while you're doing this. Pick one up from the dealer ahead of time (it's only $5, stop whining), pry/carve out the old one (it's going to be sealed in there pretty good; watch out for the spring that runs around the inside lip of the seal, you don't want that to fall into the transaxle housing), and press in (hard, but carefully) the new one. You might find it easier if you apply a bit of grease to the part of the seal that meets the transmission; it just rubbed off for me though.
One point to note here: I didn't support the hub and arms at all when I did this, but I'd probably do it next time. Just put a few blocks of wood or something under them, to take some of the stress off of that upper ball joint.
On the driver's side, you're in much better shape. You may want to make another wire support here for the halfshaft; I didn't, but that's because the engine support I used worked well as one. Once you're happy with how it's supported, you have two bolts holding the intermediate bearing to the halfshalt to the frame; remove those. Now, you should be able to slide the halfshaft back and forth a bit where it meets the transmission.
Support the transaxle. As I said above, you'll probably want a good wide jack and a transmission adapter for this. Don't jack it up or move it around yet. (You might want to do this earlier in the process; I didn't, but I'm a fatass, and needed the room to work down there.)
At this point, the only thing that should still be connected to the transaxle is the rear and upper mounts (if you haven't removed the front mount yet, take it off; two 17mm bolts). For the rear mount, I just unbolted the mount from the transaxle (two or three bolts). For the upper mount, you need to remove the five nuts holding the studs from the transaxle to the mount, and the nut and bolt in the center of the mount to release the whole thing.
Remove the one bolt you left holding the transaxle to the engine. Go over the whole area (everything should be pretty visible and familiar to you by this point) and make sure there aren't any bolts you missed; it'll really ruin your day when you're trying to separate the transaxle and engine for two hours, and realize that you forgot a bolt somewhere. (Speaking from experience.)
Separate the transaxle from the engine; it may very well slide apart easily, or you may need a prybar or screwdriver to help the initial seal break. As with the transfer case,there are a number of dowels a little bigger than a quarter inch around the bellhousing, to help you gauge how much farther they need to be separated. Check the transaxle support before pulling everything apart; are you absolutely sure you've got it supported properly (ie. along the flat base of the transmission)? You might want to ask a friend to help with keeping it steady as you lower it.
Don't pull the transaxle away from the engine very far; no more than an inch or so is needed. If you're having trouble getting them apart (the frame may be getting in the way here), try lowering the transmission and engine together, very slowly, until you're clear of whatever is in your way. Then complete lowering the transaxle (watching to make sure you don't catch on anything, like the clutch reservoir, slave cylinder, or attached hard lines), and remove it toward the front of the car. While you might be able to lift it by yourself if you're strong, don't, it'll hurt tomorrow. Go get that friend that's helping you out, and have them help you move it to wherever you need it to go.
While you have the transmission handy, put in a new throwout bearing. There are two main types: the OEM style, with a plastic inner sleeve, and the kind that comes with several popular aftermarket clutches, which are made of metal. Everyone I've spoken to recommends the use of the OEM throwout bearing; while the metal ones will work, if anything goes wrong, they will be unforgiving to your drivetrain, so you'd better understand the amount of crankshaft play you're working with and what kind of stresses the rest of your drivetrain can live with before using one. In other words, if you're reading this to learn how to change your clutch, get the OEM throwout bearing.
Installing the throwout bearing is pretty easy; take off the wire spring holding it in place (keep track of which way it was attached so you can put it back on easily), and just slide the old one off. If you've never changed your clutch, the old one will probably appear to be in pretty bad shape. I also took the time to pop off the clutch fork (there's a simple ball pivot behind it, it just pops off and slides out of it's rubber seat, which is down where the slave cylinder used to reside), cleaned it off with brake cleaner (you may have noticed a good amount of ultra-fine clutch dust all over everything; if you ever wondered where laser printer toner comes from...), applied a little "marine grease" to the ball pivot, and reattached the fork. Be sure to grease the inside of the new throwout bearing lightly as well before installing it.
Back to the car. The clutch pressure plate should be exposed now; there are six bolts around the outside of the plate, which you should remove now. I suggest having your friend (they're still around, right? give them another beer/soda/$50 for the grief you're making them put up with right now) hold a 1/2 socket wrench or breaker bar in the hole in the crankshaft pulley on the driver's side while you do this, and preferably wedge it up against something so that you can pull hard without needing them to hold it. If this isn't an option (ie. you failed to give your friend enough beer/soda/money and they left), you'll want to bend a piece of strap steel with a few carefully position holes in it to bolt to the outside of the flywheel and the engine, to keep the whole thing from turning.
Carefully pull the pressure plate and disc away from the flywheel; they're heavier than they look, so don't let it land on you.
Next, you'll have seven 17mm bolts on the flywheel that need to be removed. These are going to be on there tight (loctite is used to apply them, along with 100lbs of torque), so if you have an impact wrench handy, now's the time to pull it out. Use six-point sockets; don't try to use a 12-point socket or wrench on these, or you run a very real risk of stripping the heads of the bolts. The flywheel should come away easily.
Now that you have the flywheel, get thee to a machine shop. Have the flywheel resurfaced; many auto parts stores can do this for you, and if you're not sure, call a local performance shop and ask them where they send their flywheels. If you're using an aftermarket flywheel (in my case, I was installing a Fidanza aluminum flywheel), check with the shop you purchased it from to ensure it's stepped appropriately to the clutch you're mating up to. Road Race Engineering has a few things to say about the subject.
Now that your flywheel has been surfaced appropriately, you're ready to put it all back together (in my case, I replaced everything: pressure plate, disc, and flywheel; you may only be replacing the disc, or you might be doing just the disc and the pressure plate). Apply loctite to the flywheel bolts, put the flywheel in place (it's easy to line up; there's an eighth smaller hole in the flywheel that should match up with a hole beside the crankshaft), and finger-tighten the bolts. Now, find your helper monkey, and have them hold the crank again (or use the strap steel tool you created when taking the bolts out); this time, you're going to be putting a boatload of pressure on, though: 100 ft-lbs of torque, to be exact. (My Chilton's manual says 98, but what's a couple of pounds when you're already throwing half your weight at it?) Tighten the bolts like you would the lugs on your wheels; in a star pattern, where you tighten one a bit, then the one opposite it, and so on around the flywheel, without doing any one bolt too much at a time. If you don't, your newly resurfaced flywheel may warp.
Once the flywheel is on, use the clutch pilot tool (which should have come with your clutch if you bought an aftermarket one; if not, you can probably find one of the cheap plastic ones from any of a half-dozen performance shops) to help you align the clutch disc on the flywheel; just slide the disc onto the tool, then insert the tool into the hole in the flywheel. Leave it in place while you line up the pressure plate on the dowels on the flywheel; loctite the six bolts, and torque those to spec as well (which is a lot less pressure than the flywheel needed). Use the same kind of patterned tightening that you used on the flywheel, for the same reason.
Everything else is pretty much the reverse of what you did to get it apart. You'll likely need to lower the engine a bit to get the transmission back up in place; it was the only way I was able to properly line up the top transaxle mount without bumping against the hard clutch lines or the frame. A friend would be very helpful in the replacement; one person to jack, one person to aim. If you're like me, you probably won't be able to torque every bolt everywhere exactly to spec, because your torque wrench just isn't going to fit in every nook and cranny; it's probably not a big deal, but don't use it as an excuse to wimp out on a hard-to-reach bolt that you might otherwise be able to torque down.
Once it's all back together, bleed the clutch; odds are, it will need it. You'll also likely need to adjust the clutch: if you look behind your clutch pedal under the dash, you'll see a rod with a lock nut against a small metal square; loosen the lock nut, then turn the rod with your fingers clockwise to raise the pressure point, counter-clockwise to lower it. Tighten the nut when it's where you like it, and go in good health.
If you installed a new clutch pressure plate, you're definitely going to want to give the car a break-in period. ACT recommends 200-300 miles of driving, but keep in mind that they mean city driving, not hopping on the nearest expressway and driving a few hundred miles; if you're not stopping and going, you're not breaking in the clutch. Don't beat on the clutch during this period: no hard launches, no autocross events (waaaaah!), no spanking Hondas. Take this time to get used to your new clutch; if you installed a 2600 or stronger, or installed a lighter flywheel, you'll need the practice to get used to daily driving with it. Besides, you'll appreciate it more after the triptometer rolls over 300, and you can hit the track.
That's about it. Suggestions and corrections welcome. Thanks for reading!
I strongly suggest following the pictures in the VFAQ while reading this description.READ THE WHOLE THING BEFORE ATTEMPTING THIS. Actually, read this, the VFAQ, and the shop manual (or Haynes/Chiltons manual) procedure all the way through. Skimming all of these resources will result in you just having to read it in-depth while your transmission is hanging by a bolt and supported only by your knee and a stiff breeze.
First, you pretty much gut the passenger side of the engine bay. Disconnect the battery terminals, and remove the battery "box" (it's really just a plastic sheath over the battery) and battery from the car. There's a plastic tray underneath that just lifts out, and then there's a metal tray below that with four 12mm bolts that can be removed. There's a support frame underneath that which you might find handy to get out of your way; there are two 12mm bolts holding it to the passenger-side fender. Beneath that is a support holding some of your emissions equipment, assuming you still have yours.
Remove the two 12mm bolts holding that support in place, and push the hoses and other such things out of your way.Remove the air intake up to the turbo; this includes the flexible hose between the MAS and the turbo, the MAS itself, and the air box (in my case, a K&N filter; your configuration will probably differ). I just removed all three in a single piece; loosen the clamps on the turbo and blow-off valve dump tube, unbolt the K&N, and unplug the MAS, then lift the whole thing out in one easy piece. Don't forget about the two vacuum tubes on the back of the flexible intake pipe, and the one on the front (assuming yours are still connected). Push any vacuum hoses out of the way; the fat tube can be shoved out of the way, the tube from the valve cover can be removed completely to get it out of your hair, and the hose from the boost control solenoid below the MAS can be left hanging or removed (once again, assuming you still have any of these).
Disconnect your upper intercooler piping hose (the flexible piece between the upper intercooler pipe which holds your blow-off valve and the throttle body elbow). This may differ a bit, depending on your modifications; you may need to remove the entire upper intercooler piping setup, including blow-off valve, if you have a one-piece design. The basic idea is to expose the shifter cables.
Disconnect the shift and select cables. There are two cables that should be pretty well exposed at this point, with a small cotter pin holding each one down. The cotter pins will be pretty fragile, so be careful while straightening them. There should be a washer on each side of the cable end, try not to lose them. There are two 12mm bolts holding the cable bracket to the transaxle; remove them, and try to lift the cables out of your way. These will be in your way for the remainder of the procedure, unless you can successfully wedge them in somewhere; I didn't take my front strut bar off for this (it made for handy leverage a few times), so they were hard to reposition.
Remove the three bolts holding the clutch hydrolic line reservoir to the top of the transmission (look for a cylinder with hard lines coming in and out of it).
Disconnect the reverse light switch connector; this is a simple clip-on connector in plain sight near where the shift cables attached to the transaxle.
Disconnect the speedometer cable; this cable is located at the rear of the engine compartment, right beside the rear transaxle mount. You'll never actually see it, but there is a 10mm bolt beside the unit that the cable attaches to; run your finger down the side of the black tube that the cable attaches to (on the passenger side of it), and you'll feel the head of the bolt way down in there. Disconnect that bolt, and the entire unit will pull out (including a tall white gear at the end). When I removed the bolt, it slipped behind the engine; I didn't find it until the transmission came down. Note: I'm convinced that there must be a way to disconnect that cable without removing the speedometer cable gear, but it wasn't immediately obvious to me, and I had other things I wanted to get done at the time, so didn't get a chance to investigate further.
Remove the bolts between the transaxle and the engine. There are five 14mm bolts (three short ones, and two long ones at the front and the back, respectively), all reachable from above the car. LEAVE AT LEAST ONE BOLT IN PLACE. You don't want things coming apart early, although there's not much danger of that.
Remove the two 12mm bolts holding the starter in place. This is a bit of a pain in the neck; you might want to leave this step until after you've raised the car and removed the transfer case (see below) before doing this, as I found it damn near impossible to get at the starter from above.
Loosen the lugs on the passenger-side front wheel. Don't worry about the driver side, there's no reason you should need to remove that wheel during any of this.
Raise the vehicle. Be sure to place the jackstands behind any of the steering and suspension assembly, and raise the car as high as you can; you want enough room under the front of the car for both the transaxle and the jack (fully-lowered). Don't use the cheapo $10 jack you got from Wal-Mart; you can get the car in the air with it, and you can probably lower the transmission that way too, but you're going to hate getting the tranny back up there without a real floor jack and a transmission adapter. For reference, I picked up a 3-ton floor jack for about $95, and a transmission adapter kit (just a flat plate with some attachments for oddly-shaped items, and a post that goes where the usual round support plate goes) for about $50 at Farm and Fleet; I'm sure you could find a better deal if you shop around a bit.
Remove the front passenger-side wheel.
Disconnect the lower intercooler pipe (two clamps, one at the intercooler, one at the turbo). Remove the plastic under cover between the wheel and the transaxle (there's two or three 12mm bolts, if memory serves.
Drain the transaxle and the transfer case. See Brad Bauer's excellent explanation on how to do this.
Disconnect the bolts where your downpipe meets the O2 housing (or, if you have an O2-eliminating downpipe like me, disconnect the whole thing from the turbo). You don't strictly need to do this, but you definitely need to loosen things up so you have a little wiggle room (I didn't need to completely drop my downpipe, but I never would have reached all the bolts without some play in the piping). If you want to just remove the whole thing, there is a bolt on the downpipe ahead of the catalytic converter, and a couple of bolts holding it to the cat itself, as well as a grounding cable.
Go grab a wire hangar, open it up, and use it to create a good resting support for the rear driveshaft. Make sure it holds well; you don't want to drop the transfer case in the next step and have that joint land on the ground.
Remove the five 14mm bolts holding the transfer case to the transaxle. Three (one in front, two near the center) can be easily reached from below; the other two are positioned just above your downpipe, directly above the two on the bottom. This is where that downpipe wiggle room will come in handy. Once you have the bolts away from the transmission, use a screwdriver or small prybar to separate the transfer case from the transmission; it's not going to want to come away very easily. As you separate it, you'll see that there are a set of dowels around the edge holding it in place; they're a bit over a quarter-inch deep, to give you an idea of how far out you need to come. Careful, it can be a little heavy for a guy working on his back to catch when it separates; try and keep the rear raised, so you don't end up with transfer case fluid all over the place. Pull the transfer case toward the front of the car and off the driveshaft; it should separate easily. Make sure that you keep an eye on that driveshaft while you're pulling, to ensure that the wire hangar (or whatever you used) is holding securely.
Now for the most important step: Support the engine. We're going to start removing transaxle mounts soon, and of the four mounts holding your engine and transmission in the car, three of them are attached to the transmission. There are two approaches to this: either get a proper overhead support which gives you the most control over where you position everything, or be ghetto-fabulous. I chose door number two: a four-inch or so square piece of thin furniture plywood, with a few layers of padded rags on top of it, held in place right behind the oil supply line on the oil pan by a jack. Make sure this is extremely well-padded, and don't let anything bang against that oil tube!
Remove the gusset (a four-inch or so wide triangular structural member) and the long member running front to back on the passenger side (this differs from the VFAQ, which I suspect has an error; they mention the driver's side, but they have the passenger-side member pictured). There's about 9 bolts total, and some will be a royal pain to remove. Note that the front transaxle mount is attached to the member, so you'll either want to unbolt it from the transaxle now and take both down together, or disconnect it from the member, and remove it from the transaxle later.
Remove the 10mm bolt from the bottom of the flywheel inspection cover, which should be right in front of where the transfer case used to be. You could continue to remove the entire cover (two or three more bolts), but I didn't need to.
Remove the two 10mm (12mm?) bolts holding the clutch slave cylinder to the transmission bellhousing (there should be a hard line running from the clutch reservoir that you disconnected before to the slave cylinder, if you can't find it; you'll want to be under the front of the car for this).
Aim the steering wheel all the way left (ie. like you're turning left).
Remove the two bolts securing the lower control arm (the longish curved arm running from the wheel to the subframe just in front of the passenger-side door) to the subframe.
Remove the very large bolt on the frame side of the lateral control arm (the other, straight, arm coming from the wheel to the frame right beside the transmission). This bugger will take a little elbow grease to get out, and the VFAQ maintainer mentioned that his seized. Next, remove the bolt holding the other end of the later control arm to the wishbone/fork at the bottom of the strut.
Now for the driveshaft. There's no nice way to put it: this is a pain in the ass. You'll need a prybar; mine was a little shorter (about one and a half feet long) than I would have preferred, but it gave me plenty of clearance under the car to work with. I strongly suggest having a second person assist you with this; I was completely unsuccessful doing this by myself. You'll want to pry between the transaxle and the round green cylinder at the end of the driveshaft; while you pry (HARD) from below, have someone tap the green part from above (in my case, we tapped it from above with a breaker bar). The idea is to get a little vibration going to help settle the circlip at the end of the driveshaft in. You'll want to turn the shaft a little bit at a time as you go; once the orientation of the circlip is correct, the vibrations from the tapping to dislodge it and make the driveshaft pop right out. I spent hours on this just prying at it, and within five minutes of trying the tapping approach, the driveshaft came out. While you're prying, you might notice a rubber seal between the driveshaft and the transaxle; you will almost definitely destroy it while you're doing this. Pick one up from the dealer ahead of time (it's only $5, stop whining), pry/carve out the old one (it's going to be sealed in there pretty good; watch out for the spring that runs around the inside lip of the seal, you don't want that to fall into the transaxle housing), and press in (hard, but carefully) the new one. You might find it easier if you apply a bit of grease to the part of the seal that meets the transmission; it just rubbed off for me though.
One point to note here: I didn't support the hub and arms at all when I did this, but I'd probably do it next time. Just put a few blocks of wood or something under them, to take some of the stress off of that upper ball joint.
On the driver's side, you're in much better shape. You may want to make another wire support here for the halfshaft; I didn't, but that's because the engine support I used worked well as one. Once you're happy with how it's supported, you have two bolts holding the intermediate bearing to the halfshalt to the frame; remove those. Now, you should be able to slide the halfshaft back and forth a bit where it meets the transmission.
Support the transaxle. As I said above, you'll probably want a good wide jack and a transmission adapter for this. Don't jack it up or move it around yet. (You might want to do this earlier in the process; I didn't, but I'm a fatass, and needed the room to work down there.)
At this point, the only thing that should still be connected to the transaxle is the rear and upper mounts (if you haven't removed the front mount yet, take it off; two 17mm bolts). For the rear mount, I just unbolted the mount from the transaxle (two or three bolts). For the upper mount, you need to remove the five nuts holding the studs from the transaxle to the mount, and the nut and bolt in the center of the mount to release the whole thing.
Remove the one bolt you left holding the transaxle to the engine. Go over the whole area (everything should be pretty visible and familiar to you by this point) and make sure there aren't any bolts you missed; it'll really ruin your day when you're trying to separate the transaxle and engine for two hours, and realize that you forgot a bolt somewhere. (Speaking from experience.)
Separate the transaxle from the engine; it may very well slide apart easily, or you may need a prybar or screwdriver to help the initial seal break. As with the transfer case,there are a number of dowels a little bigger than a quarter inch around the bellhousing, to help you gauge how much farther they need to be separated. Check the transaxle support before pulling everything apart; are you absolutely sure you've got it supported properly (ie. along the flat base of the transmission)? You might want to ask a friend to help with keeping it steady as you lower it.
Don't pull the transaxle away from the engine very far; no more than an inch or so is needed. If you're having trouble getting them apart (the frame may be getting in the way here), try lowering the transmission and engine together, very slowly, until you're clear of whatever is in your way. Then complete lowering the transaxle (watching to make sure you don't catch on anything, like the clutch reservoir, slave cylinder, or attached hard lines), and remove it toward the front of the car. While you might be able to lift it by yourself if you're strong, don't, it'll hurt tomorrow. Go get that friend that's helping you out, and have them help you move it to wherever you need it to go.
While you have the transmission handy, put in a new throwout bearing. There are two main types: the OEM style, with a plastic inner sleeve, and the kind that comes with several popular aftermarket clutches, which are made of metal. Everyone I've spoken to recommends the use of the OEM throwout bearing; while the metal ones will work, if anything goes wrong, they will be unforgiving to your drivetrain, so you'd better understand the amount of crankshaft play you're working with and what kind of stresses the rest of your drivetrain can live with before using one. In other words, if you're reading this to learn how to change your clutch, get the OEM throwout bearing.
Installing the throwout bearing is pretty easy; take off the wire spring holding it in place (keep track of which way it was attached so you can put it back on easily), and just slide the old one off. If you've never changed your clutch, the old one will probably appear to be in pretty bad shape. I also took the time to pop off the clutch fork (there's a simple ball pivot behind it, it just pops off and slides out of it's rubber seat, which is down where the slave cylinder used to reside), cleaned it off with brake cleaner (you may have noticed a good amount of ultra-fine clutch dust all over everything; if you ever wondered where laser printer toner comes from...), applied a little "marine grease" to the ball pivot, and reattached the fork. Be sure to grease the inside of the new throwout bearing lightly as well before installing it.
Back to the car. The clutch pressure plate should be exposed now; there are six bolts around the outside of the plate, which you should remove now. I suggest having your friend (they're still around, right? give them another beer/soda/$50 for the grief you're making them put up with right now) hold a 1/2 socket wrench or breaker bar in the hole in the crankshaft pulley on the driver's side while you do this, and preferably wedge it up against something so that you can pull hard without needing them to hold it. If this isn't an option (ie. you failed to give your friend enough beer/soda/money and they left), you'll want to bend a piece of strap steel with a few carefully position holes in it to bolt to the outside of the flywheel and the engine, to keep the whole thing from turning.
Carefully pull the pressure plate and disc away from the flywheel; they're heavier than they look, so don't let it land on you.
Next, you'll have seven 17mm bolts on the flywheel that need to be removed. These are going to be on there tight (loctite is used to apply them, along with 100lbs of torque), so if you have an impact wrench handy, now's the time to pull it out. Use six-point sockets; don't try to use a 12-point socket or wrench on these, or you run a very real risk of stripping the heads of the bolts. The flywheel should come away easily.
Now that you have the flywheel, get thee to a machine shop. Have the flywheel resurfaced; many auto parts stores can do this for you, and if you're not sure, call a local performance shop and ask them where they send their flywheels. If you're using an aftermarket flywheel (in my case, I was installing a Fidanza aluminum flywheel), check with the shop you purchased it from to ensure it's stepped appropriately to the clutch you're mating up to. Road Race Engineering has a few things to say about the subject.
Now that your flywheel has been surfaced appropriately, you're ready to put it all back together (in my case, I replaced everything: pressure plate, disc, and flywheel; you may only be replacing the disc, or you might be doing just the disc and the pressure plate). Apply loctite to the flywheel bolts, put the flywheel in place (it's easy to line up; there's an eighth smaller hole in the flywheel that should match up with a hole beside the crankshaft), and finger-tighten the bolts. Now, find your helper monkey, and have them hold the crank again (or use the strap steel tool you created when taking the bolts out); this time, you're going to be putting a boatload of pressure on, though: 100 ft-lbs of torque, to be exact. (My Chilton's manual says 98, but what's a couple of pounds when you're already throwing half your weight at it?) Tighten the bolts like you would the lugs on your wheels; in a star pattern, where you tighten one a bit, then the one opposite it, and so on around the flywheel, without doing any one bolt too much at a time. If you don't, your newly resurfaced flywheel may warp.
Once the flywheel is on, use the clutch pilot tool (which should have come with your clutch if you bought an aftermarket one; if not, you can probably find one of the cheap plastic ones from any of a half-dozen performance shops) to help you align the clutch disc on the flywheel; just slide the disc onto the tool, then insert the tool into the hole in the flywheel. Leave it in place while you line up the pressure plate on the dowels on the flywheel; loctite the six bolts, and torque those to spec as well (which is a lot less pressure than the flywheel needed). Use the same kind of patterned tightening that you used on the flywheel, for the same reason.
Everything else is pretty much the reverse of what you did to get it apart. You'll likely need to lower the engine a bit to get the transmission back up in place; it was the only way I was able to properly line up the top transaxle mount without bumping against the hard clutch lines or the frame. A friend would be very helpful in the replacement; one person to jack, one person to aim. If you're like me, you probably won't be able to torque every bolt everywhere exactly to spec, because your torque wrench just isn't going to fit in every nook and cranny; it's probably not a big deal, but don't use it as an excuse to wimp out on a hard-to-reach bolt that you might otherwise be able to torque down.
Once it's all back together, bleed the clutch; odds are, it will need it. You'll also likely need to adjust the clutch: if you look behind your clutch pedal under the dash, you'll see a rod with a lock nut against a small metal square; loosen the lock nut, then turn the rod with your fingers clockwise to raise the pressure point, counter-clockwise to lower it. Tighten the nut when it's where you like it, and go in good health.
If you installed a new clutch pressure plate, you're definitely going to want to give the car a break-in period. ACT recommends 200-300 miles of driving, but keep in mind that they mean city driving, not hopping on the nearest expressway and driving a few hundred miles; if you're not stopping and going, you're not breaking in the clutch. Don't beat on the clutch during this period: no hard launches, no autocross events (waaaaah!), no spanking Hondas. Take this time to get used to your new clutch; if you installed a 2600 or stronger, or installed a lighter flywheel, you'll need the practice to get used to daily driving with it. Besides, you'll appreciate it more after the triptometer rolls over 300, and you can hit the track.
That's about it. Suggestions and corrections welcome. Thanks for reading!
