RE: First Things First
I don't think I'd touch engine, assuming functional air scoops make it ot production. The exhaust manifolds are essentially factory headers, much like the original 426 had, see little gain in aftermarket headers for the work.
I would probably "tweak" the mufflers (more aggressive) and most likely swap rear end gears. 4:10 w/ a 6 spd should be just SWEET.