If it were me personally, I'd grab the 2011 GT. It’s a superior car in every respect to the Cobra, save for the strength of the engine internals. In any case, it’ just as fast, or faster in stock trim and not only is it a 7-8 year newer vehicle, but you retain full factory warranty.
Yes, the ’03-’04 Cobra can be built to make and handle 550-600rwhp pretty easily, buy you'll spend as much and more on the cost of a used Cobra + supporting parts in order to reach those goals. With power like that, it should get you comfortably into the 10’s. That being said, we've already seen the 2011 GT run well into the10's with bolt ons and a little nitrous. It took $3,500-$4,500 in additional parts to do it, but you’re basically matching the strait line performance of a blower swapped, bolt on Cobra, for the same overall price, of the 7-8 years newer GT + bolt ons….and you ‘re still way ahead of the Cobra in every other category.
So my question to you is this. Are you looking at buying the best available, all around performer right now…one with a full warranty and better all around characteristics, or are you looking at buying one that's several years older, but will give you potential bragging rights later on down the road....that is if you ever decide to break the bank and tap into its full potential?