Clean the plugs and replace the wires if you haven't yet. If you recently replaced the O2 then just leave it alone. You have an A/F, or EGT guage in your car?
Make yourself an MBC and crank the boost up a bit, the factory t-25 actuator will open at about 12psi, so that's normal... If you turn it up and get more boost then you're ok, if you turn it up and it just spikes then drops off put your t-25 back on and see what happens, you might have a bad turbo.
Good luck with reading it... You checked it when it was warm right? Always check it warm and with the engine running with the car in neutral. When you pull the dipstick you'll have to hold it at an angle in the light to read it properly. ;)
Tranny parts are pretty strong, and really don't need any break-in. I would recommend taking it easy on it for about 200-300 miles and using synthetic gear oil though. :D
Only way to completely eliminate the tick is to replace the lifters with the new upgraded ones. I put 1/4 quart of Lucas oil stabilizer in and the thing only goes tick tick when I start it and thats the end of it. :D
If your car has more than 50K on it your O2 sensor is probably bad and I'd recommend replacing it, that will fix your O2 readings problem. Have you replaced your thermostat? If so what temp?
I polished mine slightly with a fine wire brush and meguiars metal polish. I got bored with it and sanded it and painted it with high temp (ceramic is best) exhaust paint. It looks sweet! Don't use an enamel. (Even if it says it's high temp!) If you want a really nice finish have it powder...