The 93 cobra and the MAF Fox mustangs used the exact same harness (comparing manual to manual anyway...)
I swapped a 93 cobra ecu into my 90GT. It's a direct swap, if it's a manual.
There is a minor difference on the auto harness, but I never focused enough on it to fully comprehend... something in the o2 harness.
If you have the blue 24lb injectors, I would say go with a 93 cobra ecu and MAF setup. If you don't have 24's, then I would use the standard 5.0HO ecu (A9L, A9P, A3m, etc...)
The Ford codes (E3ZE, etc) are not production year codes. They break down into the year of design and model that they were originally designed for. It is not uncommon for a part to have been engineered for one model, then used for several years on several other models...