Some good points so far, but there is some other info that could help you out. Since I have dropped quite a few trannies lately and replaced clutches quite a few times, a buddy of mine and I have developed quite a good method.
0) Call your NAPA (if you so desire) and make sure they have all the parts you need. Also see if they have a machine shop attached.
1) Have all the new parts and make sure they are correct. New clutch disc, pressure plate, slave cylinder (will come with new throwout bearing on it), clutch alignment tool, and throwout bearing (for $7 you might as well replace it while you are in there).
2) Make sure you have all the right tools. Sockets, wrenches, air tools are nice, but not neccessary. Pilot bearing puller, 12pt 12mm socket or boxed end of a 12mm wrench for the driveshaft, and for the hydraulic line you can get the proper tool or make due with a pair of small flathead screw drivers.
3) Disconnect everything first. Start with the driveshaft and move toward the engine. Driveshaft, electrical connections or manual connections for the t-case, speedo cable, reverse lights and neutral safety plug, shifter, clutch hydraulic line, and oxygen sensors.
4) Pull the muffler back and drop it. If you can, take off the y-pipe and cats. This will make dropping and lining up the tranny SO much easier.
5) Since you had to pull the shifter from inside the cab, here is how to make due WITHOUT a tranny jack. Make sure you have a set of jackstands that you can position on the floorboards where you put your feet on either side of the tranny tunnel. Then set a strong piece of pipe or tubing or something on them. Use a ratcheting strap to sling the transmission, putting a slight amount of pressure on it.
6) Unbolt the tranny from the motor. Should be 6 total bolts. Since it is slung you don't have to worry about it crashing to the ground. Then carefully remove it. Go back to the engine compartment and slowly and carefully lower the tranny and t-case to the ground. I usually put mine on a creeper to easily slide it out of the way.
7) Remove the slave from inside the bellhousing of the tranny. Make sure it is the same as the new one. If it is replace it with the new one that has been bench bled (do a search at
http://board.rrorc.com for more info on that).
8) Unbolt the stock pressure plate and remove the clutch disc. Compare these to the new ones.
9) Remove the flywheel. Chances are if you have never replaced you clutch, it's scorched worse than you think. For $25 have the flywheel resurfaced. People will tell you that it is unneccessary, but the one time I tried it myself with sandpaper I was extremely pissed at how poorly the clutch broke in because of the inconsistancies of the flywheel surface.
10) Reinstall everything using the opposite of these instructions.
11) Bleed the clutch system.
12) Follow the instructions on breaking in the clutch to the "T" to make sure it gets broken in correctly and will work well for you.
So there you have it. We got to the point where we could drop a tranny in about an hour and have a total job done in under 4 hours (not counting breaks, etc).