The main reason the mileage went down in '95 and up is because the body style changed, and the cars got significantly heavier.
I doubt there's any difference between the '94 ECU and the '95 ECU. In '96 the cars got OBDII, that's where the biggest difference would be seen.
Here's my advice:
Keep the '99 ECU specifically because it will permit you to use a
ScanGauge in the vehicle (the
SG requires an OBD2 computer). Using a
ScanGauge to fine tune your brain and right foot will reduce your fuel consumption dramatically more than any ECU swap you could possibly make!