Difference Between A Regular 5.0 And A Cobra 5.0??

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heads (gt40s), cam, rockers (rollers), intake, injectors (24lb), maf (bigger), computer, maybe a couple little more odds and ends. short block is the same as the lx/gt 5.0 for 93-95 (hyper pistons instead of the earlier forged ones). that said, it'll all bolt into a regular fox except the maf and computer (calibrated to each other, so use a meter calibrated for 24's with the stock a9_ pcm or run the stock 19lb injectors)
 
As stated above. Top end engine parts are the biggest difference.

Cobra and Lightning specific GT40 (non P) iron heads. Slightly different than the ones found on the Explorer.
Cobra specific intake
Cobra specific cam (actually pirated from the last 5.0L HO powered Thurderbird)
1.7:1 Roller Rockers (built for Ford by Crane Cams)
65mm Ford Racing throttle body
70mm MAF meter
24lb/hr blue top injectors
Cobra specific ECU
Post '93 HO engine, with hypereutectic pistons. 9.0:1 CR

Underrated by Ford at 235hp, but probably made closer to 275hp with that top end in the real world.
 
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unless you are dead set on going all Cobra. you can get the same HP for less money. Grab the top end off any 96-98 V8 exlorer- like gt40's head, intake flows nearly as well as the cobra/gt40, it comes with a 65mm throttle body, the yellow skinny 19lb injectors are 4 hole and flow better than the 1 hole on the mustang. You can get that in any junkyard for around 2-300 bucks or shop around. Then grab a 70mm MAF off any 1994-2000 mustang as it is plug and play for 19lb ers. If you want, throw a cam in and you are 260-280 hp . This swap has been done 100's of times. I just did it today