I did this because I was absolutely sick and tired of messing with my windows to get them to come up straight and less eletrical crap in my car. Now I can roll up my windows without needing a battery!
And for reference, the power window setup was 3.5lbs, and the rollups were 2lbs.
Tools:
Flat Screwdriver
Philips Screwdriver
10mm Socket with socket wrench.
If your battery is still hooked up, go ahead and disconnect it completely before starting.
Start with the drivers side door.
Open up your doors and pop out this little guy. Take out the screw and pop the panel off.

If you are working on the passenger side, the handle for the door also has a pop out you need to get out to get to another screw.
Next remove these 2 screws.
Then remove the last 4 screws here.
Now the panel should be ready to come off, do not yank the crap out of it, you'll be really sorry you destroyed your paneling. If it does not come loose really easily double check for any extra screws, in my doors the bottom screws at the front of the door was embedded into the carpet and you could not see the heads.
The paneling should pull off on the bottom, then lift up and out at the top.
Then you'll be happy to see this wonderfull mess.
Begin to check the window at bottom most opening, that is pre-cut for you. And your going to want to line up the window so you can easily use your socket wrench on it.
If your window is not lined up, you can use a pair of aligator clips and paper clips hooked up to your battery with the plug.
This is the passenger side plug, but you honestly cannot go wrong, just start with 1 spot being grounded and tap the other plugs till you get the window to move. These 2 spots work the passenger window, switching the ground and power makes it go up or down.
Once you get the window aligned, take out the bolts and pull the window out. It'll take you awhile to figure out how the window comes out, I had the best luck angling the window with the rear out first.
After that its just a matter of removing the door speaker, and the plastic piece that holds it in place, then removing all these bolts for the power window system.

Don't forget to unplug the motor.
Once you have all the bolts removed, take some time, and start trying to manage to get the pieces out of the speaker hole, don't worry about banging on them or streching, it is a simple system. I pulled the rail out with the motor at the same time, then the last piece came out no probs.
While you have all the crap out, take a gander inside your door, I found some rubber railing, used on the back rail guide for the window. Reinstalled it on the rail, and come to find out my window alignment problems are solved! Hurray.
Assembly is just a reverse install for the rollups. The handle uses 3 other bolts right where the motor bolts were. Install it, clamp it down with the bolts, use the handle to pull the slider down so you can get to the bolts that will hold the window into place. drop the window in, do some jiggling and it'll eventually slide on the rail. Bolt it in, and have fun. You will need to figure out where to make the hole for the hand roller, but thats remedial if your this far along.