One of the main differences is the lower intake, the stock eaton off of the cobra will not bolt directly onto your mach lower intake so make sure you are trading everyting, you will aslo want to go with the 90mm mass and and 43Lb injectors with a custom dyno tune, like DOHC otto siad the mach lower end is not fordged and also ahs a higher compression so run lower boost so you will not have detination issues, id go with 6-8lbs max.
JBA Catback, jba mid w/ high flow cats, K&N FIPK, Tri Ax, coil overs