I'm a fiend for stripes! You'd have never guessed from my Trans Am...
If you're thinking about the supercharger route, just remember that you'll have to do a bit of stiffening on the internals (insert Beavis and Butthead laugh here) to handle boost - those 4.6s really wake up though, just remember that you'll have to open up the exhaust and get 'er tuned as well. If you go with a Kenne Bell or Procharger (the only ways to go, imo), you'll probably be looking at $8-9k or so when all is said and done. WHY IN THE HELL WOULD YOU GO AND DO SOME CRAP LIKE THAT?! There's just something appealing about that front end riding high as you rip through the quarter in high 11s/low 12s...
So far as warranty goes? I'm not certain if this is still valid, but I remember back in the day, I had the option of having Ford complete and certify the installation of a supercharger (keep in mind, a Cobra is little more than a supercharged GT) and all warranty remaining valid.