So I finally got around to swapping this out. My original transmission (f5m22) dumped about a half quart of oil on the shop floor this new years day. I had also lost 4th gear completely, 3rd was on its way out and the input bearing was extremely noisy. I had the new transmission sitting around for quite some time now (f5m33).
I ended up needing to replace the cv axles as stated. The turbo ones do indeed have a much larger inner joint. I also had to change the transmission mounting bracket, starter plate, flywheel, and clutch. I discovered that the non turbo models have a smaller flywheel (same diameter as the turbo awd flywheel) compared to the turbo fwd cars and would not work with the new transmission as the starter is spaced further away on fwd turbo models. I ended up using a turbo fwd fidanza flywheel and it works perfectly. The original transmission mounting bracket was also different but I had a spare gvr4 bracket that ended up working.
Clearance was also an issue. After installing the new transmission it was slightly touching the subframe by the front diff. I removed the transmission and gently massaged (beat the shit out of with a large hammer) the subframe until I had the needed clearance. Everything now fit perfectly.
After the install was done I took the car for a drive only to notice that the second gear syncro is pretty much gone. The fun never ends