I was just going to use high temp moly grease - is that OK?  I know you pack the outer groove of the throwout bearing, what about the trans input shaft that it slides on?  Also should I put a liberal coating on the inside of the pilot bushing?  

Moly grease is good for the bearing. Use the grease sparingly...too much will sling off onto the clutch surface. The grease for the bearing, if you add any, should be put INSIDE the groove of the inner part of the bearing sleeve. Most tobs have grease in them. so you shouldn't have to add any there. Put a small amount of moly on the bearing retainer on the front of the trans.
 Don't put anything inside the pilot bushing! The bronze bushings are made of what is called "Oilite"...they have a lubricant made into them. If you put grease in the bushing, it will actually keep the lubricant of the bushing from being released...and once the grease you put in runs dry, it will stop up the pores of the bushing, and the bushing will have no lubrication...not gud.

Thanks, Joel.  I did just as you said.  Took a lot of care with this part of the project.  I've heard too many stories of the fork/bearing being installed incorrectly.  Hope I got it right....