well i think like my car almost all new auto cars except the coure have electronicly controlled transmissions. so to what i think when you xhange the tranny you will have to change the ecu as well and along with that might come the wiring and if tranny is not a perect fit to mate the engine than some mods to that maybe a mount or two and slightl possiblity o changing the shifter also. easier said then done though.
changing to manual is easier. you can use the same ecu and wirring and stuff