a 99-04 ecu can be used on a supercoupe as well, its as simple as running shielded wires from the crank trigger and using a new VR style cam sensor from a split port v6, you can either work your stock supercoupe harness or swap in a 99-04 v8 or v6 mustang wiring harness and slapping coil on plugs on her, it would probably be best IMO to use coil near plug like the LS1 setup just to remove the coils away from the exhaust
the benefit of swapping to the newer ecu's is gaining an obd-II port, they are much faster ecu's, coil on plug, the factory 2 step, and any hacks and code i write for it later down the line like CL wideband control or the nitrous/meth control like i wrote for the early sc's and the foxbody mustang ecu's