Go my transmission rebuilt by the good Dr. and went to install it this weekend. Got it installed, and after re-attaching the half shafts/CVs and the starter, I got to the part where I am supposed to reinstall the clutch cable and I realized that I forgot to install the clutch fork.
Pulled the transmission and when I went to move one of the half shafts out of the way, I extended the CV to far and a few of the balls fell out. All of the threads I found on here said they can't be put back together without pulling the axles. I'm happy to report they can, it just may take an hour or so. Thankfully, the CVs only have a few hundred miles on them so I wasn't worried about wear/ needing to inspect them.
Got the transmission in the 2nd time without issue. I think I could do it in my sleep now.