Use a 4.6 they fit better. See Sergio's site
www.cobra4me.com. Definitely go supercharged, don't go cheap on important parts, ask around here and in particular Sergio's site before you buy stuff.
Join Modular Fords site also and get into the 03/04 Cobra forum you'll find a wealth of information there. Pay attention to the blown engine thread. They are not talking about blowers they are talking about how they hurt their toys.
Very good reading You Don't Have to Hurt Yours, be informed, there is probably a million dollars of destructive testing in that one thread.
I sent you a PM with more info. Welcome to Club Cobra, the definitive place to be if you have a Cobra.
Ed