Geez I forgot all about this thread. Finished up the swap, everything went pretty smoothly overall. Wiring was pretty minor, it was so long ago I barely remember what we did, I think it was just the clutch switch and reverse lights. Once we flashed the manual ROM we were able to start the car and test everything.
The speed sensors both shit out so I ended up having to replace those as well as the front wheel bearings, and my cruise doesn’t work (I figured out the problem, I just don’t care). After the swap the clutch I had immediately took a shit so we had to replace it. The 6MT is great, the wagon is an absolute blast to drive, although I haven’t had it out in months, it’s been sitting on my quickjack for awhile while I do brakes, rear control arms and address a leaky diff.