The ABS pumps are the same in the 99-04 Cobras and GTs. The modules are different. A direct comparison can be made at fordparts.com and fordpartsgiant.com.
So, the Cobra module does work in your GT? Do you have Cobra or GT calipers and rotors?
I've been browsing this and other forums for years and just registered because I've seen the question in the subject heading asked several times (specifically for 99, 00 and 02 GT's) but never answered: Will a 2003 Cobra ABS module work in an 2001 GT with Cobra brakes - front and rear?
Except...