quite frankly if you are asking this question-means you cannot do your own wrenching & you do not have the tools or capability to do an installation yourself.
crate engine including shop labor costs and transmission, frame strengthening, chassis work, rear end, etc will be all in plus $10,000, maybe $12,000....thats without other small things like wheels, ZR tires, proper rear end, exhaust system.
to rebuild your engine-built out bottom end (rods/pistons) race heads, headers, intake, exhaust, supercharger etc.....transmission, chassis/suspension, etc, etc., etc....all in about the same.
RULE 1, unless you can do the modifications yourself- its cheaper to buy power on the hoof, there are lots of fine modified mustangs around, better to buy 1 of them - pay a little to have it fully cked out -than pay shop costs for a very difficult build.
04 cobra (modified, built out, supercharged-2.3 whipple blower @ 15lbs -measured at 575rwHP, dyno)