Does anyone know how complicated of a procedure it would be to put the supercharger, intake, throttle body, ect; of on 03 Cobra and put them onto a 99-01 Cobra?

Also, other things like the other intake peices, how hard it would be to incorporate the supercharger in the the belt drive system, and does the supercharger match with the 99-01 upper intake? If not the intake may also need to be swapped.

difficult is not the problem, expensive is. they are eaton m110 blowers, and they cost about $5000, it should not be very difficult to install, as i think all 99 and up cobras use the same block and heads, but im not totally sure.... little help guys??

I think you're correct about the block and heads. Should work.