Here is how my swap went into my 97: 01 cobra engine/transmission, engine harness, fuel rails for a 96-98 cobra or aftermarket rails, maf meter for the 24lb injectors, all the radiator hoses and the thermostat housing, cobra throttle cable. This is everything parts wise that you'll need for the swap into your gt.
The 96-98 fuel rails are a pain in the butt to get them seated properly without leaking, and the mounting tabs for them don't line up with the bolt holes on the 01 cobra lower, so you'll have to fab up some brackets. Aftermarket fuel rails would be easier but will cost you a little more.
The cobra throttle cables aren't that easy to come by either, i'd keep an eye out on corral.net, I actually got the rails and throttle cable from there. You might check svtperformance.com as well.
My engine didn't come with the thermostat housing or the radiator hoses, and they're all different. From Ford, these alone cost me $335.
You're motor mounts from your gt will work.
I kept the gt wiring harness on mine, all you need to do is swap the plugs for the fuel injectors. A little cutting, stripping and soldering never hurt anyone. Also use shrink wrap as well, this is one area where you can't afford to take the cheap way out. But all the fuel injector plugs are color coded, so its kinda hard to mess it up. You'll also need to install another coolant temp sensor if you want you stock coolant gauge to work. I didn't do this because i'll be installing an autometer coolant gauge in a couple weeks.
You're tranny and bellhousing should work fine as well.
Also, plan on a dyno tune. Unless you've heard this motor run, I wouldn't count on it starting up first thing. I never heard my engine run before I bought it and it wouldn't start after install. I loaded it and took it to my tuner to find out it had a bad crankshaft position sensor. Not a big deal. But you will need a tune for it to work, your gt tune just won't cut it. Hope this helps, if you have any questions feel free to ask, I just finished this swap in mine about 2 months ago