I really wouldn't put much faith in rebuilt engine from Autozone. If I had to buy a used engine I would go with a Jasper unit or I would buy a junkyard engine and then have it professionally rebuilt buy a reputable race shop.
BTW a remanufactuered (not rebuilt) DOHC 4.6L will cost well over $4000, probably closer to $6k These engines are not Chevy smallblocks and command much higher prices.
i know the sohc cost atleast $3-4k from autozone. Dont forget for the swap you need a wiring harness, computer, i believe different gauge cluster. It might be cheaper to swap in a 02-04 gt motor(99-01 had problems with spark plug blow out) which will drop right in, put a set of stg 2 cams and upgraded springs(needed along with a tune for stg 2 cams), longtube headers, and gears.
fodadddys right, it will cost atleast 4k if not more for the cobra motor.