well here's my logic, so follow me *disclaimer* i do not know for a fact, but i do make sense
the cobra tranny is a t-45, & the mach tranny is the t-3650. i know for a fact that the lt's on a 2v are interchangable between gt's that are the t-45 & a t-3650. i have used mac lt's on 2 different gt's, both had two different tranny's (t-45 & t-3650). so following that logic, we know that the headers fit around the two different tranny's & the exhaust ports are the same on the 01 cobra & the mach1. so i would imagine they should work. i'd call mac to make sure though