Just an update. After toying with it, I was able to reinstall the transmission cover while set for first gear. 1st and 2nd gear work in all ranges but I can't grab 3rd or 4th.
When I pulled the cover, the cam roller for the 3/4 shift fork was missing and I found it in the bottom of the case. I'm guessing the previous owner dropped it during the cover installation and managed to partially engage 2 gears, chewing something up.
I'd still be interested if anyone has any ideas short of splitting the tractor or a good resource for transmission parts if I do split it.