TF-904 is a nice transmission.
Shift kits and manual valve bodies are readily available.
The only downfall to a TF-904 behind a 2.5 Jeep is that the jump from 2nd to 3rd is a big one. I often find with steep grades that in 3rd it lugs and 2nd is revving too high.
I have 2 1995 2.5 YJs, one auto with 4.56s on 33s, one 5-speed that is stock.
The auto is an awesome rock crawler that can hang with much bigger rigs, but bogs on grades.
The 5-speed is a race car in comparison.