Good choice actually, thats what I have. You can get MIL's if you want to shut the check engine light off. I beleive you may need o2 extensions for the rears, if its the same for 04 GT's. Im not sure if you need them if you get MIL's though.
Aside from that, its a swap out swap in kind of thing. Might want to buy a 5 dollar exhaust flange gasket incase the stocker gets damaged during removal/installation.
I have weld in 40 series flows and this weekend I put in a Bassani O/R x and I love it. Not quite as much as I like it when the Bassani CB is added but that will have to wait for more $.