The conclusion that I draw from this info is the 03-04 Cobra front bumper facia is different and is the problem. This may even go so far as having a different upper core support piece. Ford and VSI are all stating the hood will fit all 1999 thru 2004 Mustang GTs. And Ford goes onto to state that it will fit all of the Cobras except the 03 and 04. That tells me that all of the hoods are indeed the same and shouldn't effect your decision on what hood you select. It's the 03/04 Cobra bumper facia that is the problem. We just need to know if it is the header or the bumper facia that is the cause...or maybe both. This also means that I will have this same issue despite buying a 2000 R Model hood.