Interesting. I was unaware that the body wiring harness was different for power & manual doors. Obviously the door is different. I'm not clear on what exactly you're swapping from the GT, beyond the engine. Are you putting the GT's power doors on the V6 body? If so, you can take the interior wiring harness from the GT and put it in the V6. This means you'll have to remove the dash.
I've got a Ford electrical manual, and there are three types of connectors for each of the two plugs for the driver's door; and they don't interchange with each other. From what I can tell, they depend if you have:
* A coupe with all options (power doors & windows, keyless entry and anti-theft)
* A convertible with all options
* A coupe with anti-theft only (probably your V6)
From what I can tell, the V6 manual harness has a connector with two rounded corners, while the GT's harness is square. The other connector is square for both, but has different slots & alignment grooves so you can't connect the different types together. I believe the coupe and convertible doors have different harnesses as well, since the 'vert's door window switches control the rear quarter windows in the back.
You might be better off swapping the entire interior wiring harness between the cars.