Decided to divorce the transmission and tcase.
Very sorry to hear you made that call when you were already extending your job time farther out than you wanted. I'm sure it was just to make things easier to move around, but it was literally asking for trouble.
Now you have to disassemble the transmission.
Easy enough, but I bumped it out of first and the bearing on the back of the transmission shifted out and the shift levers will not move much now. What did I do now?
Sounds like you knew to put it in first, but were you aware you had to "lock" it in gear? Supposed to fabricate a tool out of 3/8" rod, but you can also zip tie things in place.
Unfortunately even with a pair that have recently been separated, all it takes is a little English between them to get the output shaft to stick and pull the bearing and shaft out, dropping the bearings that were mentioned. There is only a little bit of leeway (maybe 3/8" or so?) and after that things happen quickly.
They are basically the loose roller bearings that are retained in the recessed area between the input shaft and output shaft, and how the two shafts are supported in the middle to do their thing.
They just fell out and into the bottom of the transmission case. Easy enough to put them back in with a little grease to hold them in place temporarily, but you have to pull things almost completely apart to do it.
Also, I realigned the clutch, the alignment tool slides in and out easier now. However, my buddy and I tried to slide the transmission in without the bell housing and it is still an inch away from fully seating.
That's maybe a good thing, but the tool moving in easier does not necessarily mean it's perfect. Hopefully the only thing working against you is the clutch still slightly misaligned.
But I would use a bright light to peek inside the pilot bearing and make sure nothing is inside that could be blocking anything. No burrs on the bushing (is it a bronze bushing or a needle bearing type?) and no grease.
If you packed any grease in the pocket you could be blocking yourself with hydraulic pressure.
Again, the only thing I swapped out was the flywheel, so the parts I am trying to put together, were already together.
That's good news, but should definitely look up inside the end of the crank to see if anything got lodged inside.
When you get to the point of installing the trans for good, with the bell housing in place, you may find it handy to have an extra jack to hand to lift the front of the engine up and tilt the rear lower. Or just do it ahead of time and hold it in place with something.
Good luck! Sorry to hear you're having to go to so much trouble.
Paul