Harwood91,
I'm not too familiar with the '01 Cobra to '04 GT tail light harness swap, but I would imagine it would be pretty straight forward. Even if it's not a plug-and-play option, some simple soldering of a few wires in the trunk should be all there is. I know it's not more extensive than working with the wires right there in the trunk.
Hopefully someone else can chime in who has done this already and give you more detailed directions. Let me know how you make out!
Shane