Some quick help please

You know what; I just thought of something.
If your guy was spinning the M/S while it was still in the rear housing, and no rear yoke installed, then, if that rear bearing looks anything like those gears, then there is a good chance that the M/S nose was doing a dance, which could be interpreted as "warped". This is, of course, a bs way of testing.

That's actually a really good point. I went to the transmission shop last night, but the guy who's working on it wasn't there. I did look at the gears though. They looked worse in person than in the pics. I couldn't tell if the main shaft was warped or not by looking at it, but it looked worn too. He did give me the number to a guy that says he has what i need. I spoke with him, and he was willing to sell a main shaft, all the gears, and synchronizers for a couple hundred, which is cheaper than he originally said for everything.

Looks like it's going to be a full rebuild with a new clutch, I also took the flywheel to Napa to have it turned, so she should drive really well when i get it back!