The 4.6 is the new car. 2006 GT. It's an automatic. My 1993 GT is already supercharged. Vortech S Trim. It's the classic now. Its faster than the 06. (For Now).
Since its an 06....I would post in the 05+ threads. Its a whole different moddin' world for the 05+'s. And from what I've seen...a CAI on an 06 would be a good mod, but will probably need a tune.
Oh, ok. Best first mod for this probably would be a SCT Xcal2, maybe bundled with an intake pipe/air filter package. That's what I would probably go with.