Heh, I just went through this not long ago, I'm converting a 94 V6 to a Cobra. The wiring harness that leads to the computer is different, it leads all over the passenger side of the engine compartment. The wiring harness that crosses the radiator and leads to the fuse box is the same for V6/GT/Cobra. The only difference in the wiring is if you have ABS; the non-ABS harness is short a couple of wires.
I recommend pushing the harness for the computer through the firewall behind the fender, rather than running all the wiring from inside the car through the hold in the firewall.
I'd be happy to answer any questions you have about the swap, just IM me or post it here.