Are you looking at a 4door or 2 door?
If you were close to me I would start pulling the manual trans and pedal package yesterday to swap, I despise any manual trans on a offroad vehicle!
The 3 speed auto and 5 speed manual are basiclly directly interchangable, both are the same length and use the same transfercase and will bolt up fine. The pedal packages should also interchange. There may be ECU/wiring issues, but nothing that cant be worked around.