The first mods that will provide the best bang for the buck without requiring any special tuning would be CAI/Cat-back/X-pipe. Those three alone are good for 400RWHP usually. Are the flowmasters just welded in mufflers or is it a complete
Flowmaster cat-back? You really want to get a quality high-flow 2.5 inch exhaust system on these cars if you want to make good power.
After that look at getting a good hand-held tuner (Xcal 2). It will allow you to release a few more ponies, but more importantly it will give you a platform in which to transfer custom tunes into your EEC once you decide to go with a smaller SC pulley.
U.M.
Please take 10 minutes and read this 03/04 Cobra FAQ. It will answer 99% of the questions a new Terminator owner may have.
03/04 Cobra FAQ