The basic reason you don't want to install a non-Ford motor into a Cobra of any stripe is that you're going to knock one third to one half off any resale value. Look at past sales: nothing knocks off sales value like a Chevy engine. It's absolutely no knock on Chevy or any other maker, it's just that the market dislikes unusual engine and driveline choices (an automatic tranny is almost as big a price downer).
Don't build something as expensive and exotic as a Coupe and either try to save money or express a very contrary preference by fitting it with a non-Ford engine. Don't believe me? Go back to the GM forums and ask around about fitting a Ford 429 in a Vette.
You're also looking at a helluva lot of mods to the frame, mounts, exhaust, and probably cooling, intake, ignition and maybe even body. Bottom line, you'll spend a fortune in cash, sweat, blood and tears to build something that's a 50% loss, when you could much more easily build a desirable beast that sells for something close to what you put into it, when you decide to move to the next project.