Anybody with a 99+ cobra and magnapacks?

IMHO, yes it can be done, but you'll have to tinker a little bit. It wasn't as simple as purely swapping them out & re-bolting things back up.
IIRC, a fellow '01 owner had to have an exhaust shop use a "pipe expander" in order to get a good fit for joining the Magnapack mufflers into the rest of the Magnaflow catback (he was in the same situation you are)...so, don't be surprised if it takes a little work, but it CAN be accomplished - not a big deal! :cheers: