Alot of people recomend pulling the motor and tranny for a clutch job. Personally I find it much easier to just put the car on 4 jack stands, loosen the motor mounts, and take the tranny out by its self. The top two bolts are easiest done with a few feet of woobly extensions from the rear of the tranny. You can try from the top with a combination of a few wrenches together, but it'll cut up your fingers.
Make sure you do the rear main seal and tranny input seal while your in there. Grease the splines where the pilot bearing slides, and the slave lever dealy thing.
Use the allignement tool and keep it in till after you torque the pressure plate.
Tq the flywheel bolts to the correct ammount. They make a tool that will grip the teeth of the flywheel while you tq them.
Drain the tranny fluid before you take it out.
When you take it out be sure to take off the bolt on the front side of the stater that bolts it to the bracket on the motor mount. I always forget that one.
Undo the wiring harness from the top of the tranny. Also make sure to take out the shifter when you do it. You don't have to completely remove the ppf, just take it off the front and loosen the diff bolts. That way you wont have to worry about disconecting the wiring bundle from it.
There are two wires on top of the trans I would mark which is which (when you see them you'll know what im talking about) so you don't cross them on re-installation. I don't what happens if you do but its easier to just avoid finding out.
Make sure you have all seals, gaskets, grease, trans oil, boots, etc. that you need. It's a good time to just replace all that stuff.
The top right bolt of the trans I found was easiest to get to from the top. I just unbolted the tab that keeps the hard lines in place and moved them a bit to the side, and bam instant access. Worked for me at least.
Don't over grease the spindle area of the trans. I had a friend do that and it ruined his clutch.
Yep slave cylinder will be done at the same time. I have a new shift rebuilt kit thats going in when I do the clutch. Im at the point that I want to do it once and get it all done. The car needs some TLC so pull the motor, (maybe new mounts if in the budget) and replace all the seals and clutch/flywheel etc at the same time seems to be the way to go. So much good info thanks!