It would seem to me that you would want to start with the stongest base possible. The DOHC 4.6 in the Cobra is pretty stout despite what alot of people believe. If you go with the GT you're gonna have to dump a lot more money ( I would think) than starting with the DOHC and going from there. You can find older late model Cobras at very decent prices so older Cobras are roughly in the same range price-wise as a late model GT. Cobras are cooler IMO.
That's a good chunk of change so you should have no problem no matter what you decide.
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66 Tahoe Turquoise Coupe
Laser Red 96GT Ragtop
30 Years & 30 inches apart in the driveway!