Don't use Pypes, they don't fit right. Otherwise there's not much difference in performance what ever you pick.
The most important thing to do is get rid of the stock V6 muffler, it's very restrictive, only 1 3/4" interior diameter.
After that what ever muffler and setup ( X, H, or Y ) you pick will all be similar exempt for sound & looks. The stock GT mufflers sound very good and not too loud, the Bullitt (M-5230-GTB) mufflers are a little louder than that, and the M-5230-GTA's louder still.
I used an H on my '06 (cut/weld) and reverse Y (Mac bolt-on) on my '10... absolutely no difference. both with '05-'09 GT manual (Fl-7841-L/R) mufflers.