Okay, a lot of this is off the top of my head but here goes: These are the differences that set the Cobra motor and Explorer motor apart from the "standard" 5.0 HO motor.
1993 Cobra: Specific "Cobra" intake, cast iron GT-40 heads, 1.72 roller rockers, 65mm throttle body, 70mm mass air meter, 24 lb injectors, Thunderbird 5.0 cam (F3ZE), Cobra specific ECM.
Explorer 5.0: Specific "Explorer" intake, GT-40 (96') or GT-40P (97' up) heads, standard rockers, 65mm throttle body, "high torque Explorer specific cam (F4TZB), and I don't have the injector or mass air specs! Sombody help with that.
The 5.0 roller cam engines are, for the most part, all built from the same 9.0-1 CR short block, but then receive unique top ends, cams, and computer tunes.
The X motor and 93' Cobra motor are very much alike. Somehow a near identical parts array make 235/280 in the Cobra and 215/288 in the X, however, the 93 Cobra is notoriously underated. I would say that exhaust, cam, and computer tune is where the X suffers. After all, the GT-40P headed motor is rated at 270HP (with an E cam) when sold as a long block crate engine by Ford Racing. The standard 87'-92' 5.0 HO was rated 225-300, and that is without all of the GT-40 top end inprovements!
Hope this answers a few questions, I am sure others will have some details as well.