First mod is a good quality CAI! That one mod alone can achieve some awesome gains on this car. (up to 20RWHP!)
Next best mod is a cat-back. Then a custom tune. Ford left a bit on the table with these cars.
Skip the mid-pipe for now... you don't gain a lot from them on these cars. I'm not sure whether a O/R mid-pipe from 2000 GT will be a direct swap or not.
U.M.
P.S. Have you read the 03/04 Cobra FAQ located at the top of the SVT Tech sub-forum? It answers almost all of these questions and more!