The pilot bearing is in the end of the crankshaft and the tranny input shaft rides in it. When redoing a clutch you need to line up the disc with the pilot bearing so that the input shaft can slide into both. If they are lined up, the trans won't slide forward enough to bolt it up.
What you need is an alignment tool. You can either buy/rent/borrow an generic one, or if you buy a full clutch kit it should come with a plastic one that will fit. It has a tip that just fits in the pilot bearing, and a wider part that just fits through the clutch disc, and centers to the two to each other while you bolt the pressure plate on.
No flexplate on a manual trans, the flywheel sits right where an auto trans flex plate would be.
If you have it apart and can spare a few bucks(~$100), do yourself a favor and get a full kit. If the flywheel has no grooves you can reuse it, but it would be best to get it resurfaced at a machine shop. If nothing else, get a new friction disc. (~$30)
Be aware that if you swap a different motor into an 80 4x4, the flywheel and all the clutch parts may be different. The 80 4x4 uses a bit larger disc than the 2wd 80, and all older LUV motors. Be sure to swap all the parts to your donor motor.
Oh yeah, if you take off the flywheel, use blue locktite on the bolts when you put it back on. Otherwise oil will weep past the threads. Might as well replace that rear main seal too...
