Matt - the fact that Shelby may or may not have approached GM for an engine is immaterial. He did not get it, and the Cobra had Ford engines exclusively during it's original reign.
Look at it like this - you had a 50/50 chance of being born a woman. Should you now wear a dress?
I personally believe that the Cobra is synonymous with Ford, but of course, that is just my personal belief. You go build your car however you like it's your car, your money, your dream. Just don't want you to spend the rest of it's existence trying to justify why you put the "wrong" engine in it.