Thanks to all who replied.

Likely damage from not installing the upper bellhousing bolts are:

cracked case
bearing damage (release bearing?)
thrust plate damage
flywheel damage
bent input shaft (transaxle)

This is what I have found on my Bus:

slightly bent fork on release bearing throwout arm - caused two new release
bearings to fail before problem was detected.

worn out clutch release bearing throwout arm bushings

damaged pressure (thrust) plate

I replaced all of the clutch components, bent the clutch fork back into
shape, replaced the bushings, and installed the upper bellhousing bolts
too, but the clutch system failed again after about 1000 miles.  This is
the third time in less than a year that the clutch has failed.  I am almost
at a loss as to what to do next.  I plan on replacing the clutch release
bearing throwout fork with a good used fork, and also replace the
flimsy-looking stock release bearing clips with heavy duty ones from Rocky
Mt. Motorworks.

  I'll still be afraid to drive the Bus anywhere.  I was a ways from home
when the clutch went out in the Catskills, and I don't want to repeat the
nerve-wracking, clutchless drive down from the Catskill Mountains to
Albany.  (yes, you don't really need a working clutch, but I find that it
is more relaxing to have one)

When the engine was mated to the transaxle, it was flush with the transaxle.  

How can I tell if the input shaft is very slightly bent?  Wouldn't there be
some difficulty shifting gears?  Wouldn't there be vibration and noise?  I
haven't noted any of these symptoms.  I strongly suspect that the lazy
bonehead of a previous owner caused the damage to my Bus's clutch by not
installing the upper bellhousing bolts that secure the engine to the
transaxle.

Wolf