CAI is worthless, the tune is what gives you the power bump, dont' fall for advertising that tells you otherwise. Bama is not the greatest tuner in the world, there are plenty of ppl who will actually datalog and burn you a custom tune via email vs just a pre-canned tune they send to everyone else who has a similar combo to you.
For a S197 I'd get a full catback, midpipe, gears, shifter, and then tune it. Then suspension/wheels/tires. The 3V isn't exactly world beating performance wise espeically when lightly modded 2V cars can run with them pretty easily. IMO, the biggest benefit going to the 05-up is the chassis and interior, not the motor.
2000 Mustang GT Steeda #0048 34k miles. 99 Cobra 4V swapped, FTBR IRS swapped, exhaust, tuned by James Gordon.
Just because I give you advice, doesn't mean I know more than you. Its just means I've done more stupid ****.