This, I hope, is the final post on our transmission failure.
When we discovered that the C6 thrust bearing came apart inside the transfer case, we decided it was necessary to take apart the whole transmission to see where the bearing parts went, and if there was any additional damage. Once done, we were relieved to find that the damage was exclusively in the C6 clutch, and that the rest of the transmission looked to be in great shape. We figured there were approximately 40 roller bearings floating around somewhere in there, and we found about 3 of them in the C6 clutch, and another 30-something in the screen on the intake side of the scavenger pump. This screen is behind the elbow that the hose of the scavenger pump attaches to at the side of the transfer case.
We have a Stewart & Stevenson in Albuquerque, but they did not prove to be very helpful for military truck parts. However, they are also the Allison transmission distributor, and were very helpful in ordering the parts we needed for the transmission. They printed out all the parts diagrams and parts lists for the transmission after we gave them our serial number, and we were able to order replacement parts based on these lists. Xcalliber Transmission online also sold us some of the parts we needed; one part was used (the C6 clutch cover/housing), some were new Allison parts, and others were aftermarket, but made by Xcalliber. Allison genuine parts can literally cost a fortune, so we were happy to have an alternate source for them.
We put the truck back together yesterday and took it for a drive, and it seems to shift through all the gears just fine, with no error codes. We had never taken apart any transmission before, much less an automatic of this size, and used the TMs to do the work. We did have to buy a big transmission jack, a big engine stand, and a big impact wrench to do the job, but we like that better than paying for someone else's labor. Thanks to everyone on here who steered us in the right direction.