01 cams have different duration and are better suited for upper rpm/hp. The 03/04 cams are better designed for low - mid range TQ. Yes you can use them in your cobra. It's just a matter of if it's worth the $$. Teksid are 'traditionally' stronger blocks that WAP's. Some would disagree.
There is a thread below that list the difference between machs and 99/01 cobra's.
And no, the 99-01 cobra's dyno a tad less....however, it's fairly minimal. The difference is mostly in the low end TQ vs. the upper HP of the cobra. THe machs heads flow better, different intake, better gears and solid axle.
EDIT: here.... http://www.svtperformance.com/forums/showthread.php?t=537174
Thanks for thread link, I checked that out and found an answer to yet another question I had about 01 cobras; Friend of mine has a stock w/18k miles for sale, It has a Teksid, and I wasn't sure if it was a replacement motor.
Actually, DID that thread really address that question about end of Teksid, beginning of Wap...O.K. I'm still unsure. Oh well.