Some run the '03 Cobra clutch & flywheel in thier '96+. Most haven't had any problems. It grips well and has a good feel. You're going to need new pressure plate bolts. The 11" clutch uses a different size. The part number in the Ford computer is wrong (unless you want to find that out the hard way). The part number you need is N808969-S100. They come in a package of 6 from Ford.
You'll really enjoy the aluminum flywheel. Once the tach sweeps past 3500 the motor will rev much quicker than before. Total weight savings from the stock 96-98 stuff is 8 pounds, so 99+ should be the same, and you'll feel every bit of it.
Stock ’96 parts-
Flywheel = 21.5 lbs.
Pressure Plate = 18 lbs.
Clutch Disc = 4.5 lbs.
Total = 44 lbs.
’03 Cobra parts-
Flywheel = 12 lbs.
Pressure Plate = 19 lbs.
Clutch Disc = 5 lbs.
Total = 36 lbs.
I'd post stuff like this in tech tho if you want some solid opinions