You heard right; the 99 Cobra was the one with the horsepower problem, it had about 305 (instead of the advertised 320) until Ford fixed them. The '01s had an honest 320. The Mach 1, also with an aluminum 4.6L DOHC, was making 340, so that would give them an advantage. The Mach 1 also has a live 8.8 versus the Cobra's IRS, and both have their ups and downs, but the stick axle would be better for drag racing. If you want to hop up either of the Cobras, I'd start with the standard stuff, cold air kit, exhaust, chip, throttle body, fuel system, etc. If you want to stay normally-aspirated, then better heads-cams-intake are available from Ford Racing. Take that much, and a modest nitrous kit, and you should have enough power for anything you want to do. If that isn't enough, most of the major speed parts vendors have kits for any of the power adders you'd care to choose from. Based on '03 Cobra experience, I'd recommend one of
these from Kenne Bell, the low-end torque is worth the extra money over a centrifugal kit like
this or
this. Good luck, I hope you find something you like. Jim.