my Buddy is doing that swap, you are going to need a manual ECU, you can cut the engine wiring harness apart and remove the auto stuff (but you should check that all of the other wires in the harness go to the same place on the ECU in the auto. and the manual trans. you can get that info from the FSM) I'm almost positive that they do.
save the oil presher sending unit from your 3.0, and put it on the 3.4 it will bolt right up(if you use the 3.4's OPS you will fry your oil presher gauge)