Interesting question. I'd expect that the ECUs are of the same class, that is, the connectors would be the same, and likely most of the connections on the same pins. The issue is the sensors on the EVO3 and the 6-bolt engine. If your EVO3 ECU is a JDM model (as I suspect) then there's more chance of unexpected differences.
The only way to know for sure is get the wiring diagrams for everything including the sensors, and create a cross-reference table. Some sensors will be the same, but there's also some signals (e.g. the tach waveform) that have opposite polarities (i.e 0v->pulse high vs 5v->pulse low) that changed sometime between 1990 and 1993. Then there's the cam angle sensor and TDC sensor that change sensor type and location between 6 bolt and 7 both engines.
SD
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