I'm sure somebody else knows more about these engines than I do., but off the top of my head:
OBD-II started in 1996. A 94-95 Mustang GT had a 5.0, and no 5.0's came with the OBD-II.
The 94-95 5.0 had a unique upper intake with the the throttle body angled off towards the front of the car. You can use an earlier upper intake with an adaptor, but in a Cobra it doesn't matter. The 94-95 engines had less HP, but I heard that this was totally due to the less aggressive spark curves in the ECM. The 92-95 engines had hypereutectic pistons rather than the forged pistons of the earlier engines. The hypereutectic pistons are supposed to offer better
oil control because of tighter fit and less piston slap at startup, but they aren't as strong. All the 5.0's have roller cams. The later engines have a less aggressive lift ramp to help quiet valvetrain noise.
All the 5.0's have low drag rings, and I've seen engines with 100,000 miles on them have no cylinder ridge and still a cross hatch visible. If you're putting it in Cobra, most of the 87-93 stuff will fit.