first the fit is rather tight, but quite doable. i recommend swapping to 66 mustang mounts as they set the engine a bit higher in the engine compartment making header clearance better. use a good set of shorty swap headers as they will fit better than long tube headers, and you wont notice the performance difference. use a performer rpm intake with an edelbrock carb and a drop over base air cleaner for hood clearance. again it will be a bit tight but this combination clears the hood. if you have any qualms about ubsing the rpm intake, then use the regular performer intake as it is even lower. when you swap to a 5spd, i highly recommend that you also swap to a cable or hydraulic clutch system, as the stock linkage tends to bind. consider installing an electric fan to replace the stock one as you can gain some clearance between the engine and radiator. use a good 3 or 4 core radiator, i prefer copper/brass rads but if you want an aluminum one make sure you get one with at least 16 fins per inch, and two rows of 1" or 1.25" tubes.