Made a little more progress tonight, got the new shift fork installed, cleaned the transmission, adapter and transfer case up in the solvent tank, not perfect but definitely cleaner. Mocked it all back together to make sure I had the transmission top plate assembled correctly. All seems to be working correctly. Now I'm waiting on a throw out bearing rebuild, the new motor mounts and a new radiator since the previous owner put a nice sized hole in the one in it now.
Broken shift fork, $20 fix.
All mocked back up.
For anyone wondering this is what the adapter from the T5 to Toyota transfer case looks like.