Yes, it is true that the 03-04 Cobra hood and 99-up GT front bumper fascia are NOT a perfect match. You can put on the hood no prob, but there will be a slight gap between the leading edge of the hood and the front bumper.
I was going to do this myself when I had my GT and the fellow at Carolina Mustang told me that a good body shop could make it look pretty good, but I didn't like the idea of "making" something work that wasn't really designed that way.
Sean Hyland was at one time working on a reproduction Cobra hood that was designed to work with the GT fascia, so you might want to give them a call and see if they ever actually saw production.
BTW, the people at Ford Racing verified the slight incompatibility of these parts when I talked to them about it, so this info is pretty solid :thumbup