While it's disassembled:
Machine flywheel
Replace rear main seal and inspect crank for groove (use speedi sleeve if necessary)
Replace pilot bushing (it's a bushing, not a bearing)
Replace disc and pressure plate
Replace throwout bearing
Take the opportunity to clean the bellhousing and transmission
Reseal transmission (input bearing retainer & bellhousing-the bolt holes are open to gear oil).
Replace jackshaft nuts (there are plenty of threads explaining why).
Remember to mark the flywheel, as it only goes on the crank one way.
I used loctite on flywheel and pressure plate bolts.
Tech manual describes how to adjust the clutch linkage (there is a procedure).
Use a takeout input shaft to align the clutch disc-my clutch aligning tool was insufficient and I had to pull everything back apart and re-do it.