The tranny and T-case comes out first. Then the pressure plate is unbolted which frees the old clutch disc. Next the flywheel is unbolted from the back of the crank. At this point it's a very good idea to check for any signs of rear main seal leaking. If it's leaking even a little you might as well replace it as you've done 90% of the work for that job already.
Check the flywheel for heat scoring and or cracking. As long as it's not too messed up it can be re-ground. Cost is usually around $30-$50 to have that done.
Re-install the flywheel. It can only go one way as there is a dowel to position it. Use a torque wrench to get the bolts properly torqued.
Most every clutch kit I've bought over the last 15 years has had a dummy input shaft to align the clutch disc during re-assembly. You slide the dummy input into the clutch disc, then slide the small end into the pilot bushing. This holds the clutch disc in position until you get the pressure plate bolted up. The pressure plate bolts should be tightened equally in increments, then torqued.
I then re-install the bell by itself and torque those bolts up. At this point I put the new throw out bearing on the release fork. Make sure it's facing the right way...best to pay close attention to how the old one came apart.
The last part is the hardest part of the job...and that is getting the tranny re-attached. The input must go through the throw-out without dislodging it, then through the pressure plate (without bashing any of the release fingers) and finally the splines must pass through the clutch disc. This is where it can be frustrating.
I specifically bought some extra long bolts that fit in the bell and use them as guides. You get the tranny started, thread in the long bolts and continue. Once you're at the clutch disc the fun begins. If you're smart you'll put the tranny in gear before you start the process, and find a gear that allows you to rotate the tranny using the rear yoke. once you get the input against the disc rotate the tranny a little while gently wiggling and pushing the tranny. Getting it to go through the disc has taken me as little as 5 minutes, and as long as three hours of wrestling.
I prefer using an engine hoist through the tranny tunnel over any sort of macguyver'd floor jack method.
Oh yeah, you'll want to remove the shifter. Twist the retainer collar while pushing down and the shifter will pop right out.
Rene