I did a quick search and from what I can find it says the cobra uses a 4 channel output where the GT uses a 3 channel but this is just what I am finding from google searches.
Ford used 2 distinct ABS systems on the 94-04 cars. The early cars had a 3-channel ABS system. This setup ran from 1994 to 1997. 4 inputs from wheel sensors, but only 3 outputs. Single line to the rear. This system uses a diagnostic port under the hood to pull ABS trouble codes, and you can use a paper clip to get the ABS light to blink codes. In 1999, Ford went to a 4-channel ABS system across the board, with traction control. The algorithm was improved and this is thought to be a much better setup. The system now is module based, so DTC's need to be pulled via a scan tool that can read module-based DTC's. Now, i haven't been able to confirm this, but 1998 may have been a crossover year. Early cars got the older 3-channel setup. Later cars got a 4-channel setup (minus the TC). I'm not 100% on that.
My understanding is the difference is in the programming of how the system responds due to the differing brake setups/rotor sizes and predictive braking. The Cobras have larger brakes so they are able to exert more braking force to the rotor and can slow down the car at a faster rate. Because of this, the Cobra units have different program to take this into account and predict lockup for their unique brake setup. There's a few modules: COBRA, GT Traction, V6 traction, and V6 ABS
But I put full Cobra F&R brakes on my previous '03 GT without issue, and currently have Cobra front brakes (rears coming soon) on my '00 GT and they operate normally as far as I can tell.
