What do you need? Pretty much the entire donor car. There are so many parts you will have to take it doesn't make sense to order them all. I've seen the parts list its over a page long. Also need a new kmember for a modular from maximum motorsports. The cobra is a 4.6 not a 5.4. A 5.4 is a truck motor.
go get a wrecked 96-04 GT. swap the K-member and the dash wiring, ECM wiring, Fuel lines, fuel tank, radiator, and about everything else (don't have to swap the dash itself, just the cluster), the hydroboost brakes, might as well upgrade to 5-lug, so the front and rear suspension, swap out the A/C evap. so you can have A/C. It will fit in a Fox HVAC box, and get a good wiring diagram.
You would still be missing a ton of parts. The GT will not have the correct fuel system, tranny and heat exchanger parts. It really is best to use a donor 04 cobra, or it will be a headache.
A mod motor swap isn't so much a job of putting a mod engine into a Fox, its more putting a Fox onto a mod motor if you catch my meaning. When it comes down to it, the only Fox stuff you'll have left on the car is pretty much just the shell, haha. Check out SVT32VDOHC's progress threads for some good info.
You could do it with a stand alone engine management system and a custom fuel system... thats the easiest without a donor. otherwise you need something with a return style fuel system so 98+
get the harness from car is coming out of. the 2v and 4v harness is different. and if your using a t56 from a 04 cobra you also need the trans harness since it has a rev lock out (found out the hardway on a mach1 t56 swap)
the k memeber can be out of any 96-04 gt or cobra....
Where did the OP go? A 2003 Cobra has a 4.6L, not a 5.4L You can put that into a fox. A friends Dad put a 5.4L 4V Navi motor into his fox. He hand made a custom intake for it and ran manual brakes. He eventually installed a brake booster where the battery is supposed to be and made his own brake lines. He said it was a big improvment over the manual brakes, but it still didn't stop well. You really want a donor car to get the hydroboost set up. I'm not even sure if that would fit. The 5.4L 4V heads are much larger than the 4.6L 4V heads.