I know Ford ECU's aren't locked to a certain car. But as far as using a GT ECU in a Cobra, one's a 2v and ones a 4v. They cannot interchange in stock form. You may be able to flash it and put a tune on it but I'm not even sure you can do that.
The ECU codes vary among years like 96-97 have LLX# and the 98's can have AOL# So the ecu will not have that vehicle's vin prgrammed into it (because of resale or the availability of that ecu as a replacement for another car), but the ecu code itself represents that ecu belonging to a certain year car.
hes talking about his OBDII Readiness check. im gonna assume you tried to smog it and you cannot because the readiness codes.
IIRC you can have the dealer reflash the ECU and drive straight to the smog place or something like that.
ECU's are interchangable but must be from the same year as well. and no, a 2v GT ecu will not run a Cobra/Mach1, and the pinouts are probably different as well.