Well I'll try to give a little sound advice here but don't take it as gospel as I am far from being an expert.
Supercharging. I think the only way you can get factory warrantied work done for a supercharged car is to have one of the Authorized Ford tuners do the complete install and everything for you. (Roush, Saleen). As for a do-it-yourself mod, the only way a warranty claim can be denied is if they can prove that the mod caused the failure. ie.. tehy can't void your anti-lock breaking system warranty because you put a X pipe on your car.
As for modding the car in general and my personal opinions to it. I'm going to do ONLY engine mods. Meaning.. no forced induction (Turbo/supercharging) no NOS or other easily catastrophic mod to the car. Going the "Engine" route.. heads, headers, forged internals, intake, exhaust.. you stand to spend a bit more money and it will take a bit more time to accomplish than bolting on a Paxton, but you'll have a solid engine that performs. You won't have to worry about Nitrous nuking your intake.. or a supercharger taking out your pistons/crank because you ran a little too much boost. There are people who run this stuff safely.. don't get me wrong. But for my dollar, and for the hopes of keeping this car for many, MANY years I'm going to err on the side of safety and go with mods that will not only make my car a stronger performer but also make a stronger car.
Hope that helps you out. :smile: