Just a quick update. I picked my transmission up on Monday, fully rebuilt and ready to go! The carrier bearing on the loaded side was toast. He replaced all the bearings and the synchros and inspected everything, everything looked good. Only thing he found as a possible culprit was the preload on the diff was 0.016" too tight!
That could have lead to premature failure of the bearing, hard to say for sure.
Also, I decided not to change the gearing. I had thought about going with an 0.89 4th (from 1.04) for better freeway cruising, but I decided to stick with what I have. I love how punchy the car is even in 4th gear, and didn't want to give that up for rare freeway drives. I'll just continue to put up with 3750 RPM at 65 mph on the freeway.
I still have a bunch of little things to do before putting the transmission and motor back in, but hopefully I'll have her back on the road in a couple weeks tops.