Actually to my understanding, ECUs go something like this:
86-87 2.5 = different between auto and manual tranny
88-89 Sedans/87-89 Coupes with 2.7 = difference between auto and manual
90 Sedans and coupes = Different from all other years in pin-out and different between auto and manual
From what I have heard over time on this forum also, is that an auto ECU can be used for a manual transmission car, BUT a manual ECU CANNOT be used on an auto.....but that might only be for 2.5's I dont quite remember....
Also...
While the programming may be the same for certain years....the ECUs are physically different...the coupe has the sight glass for the red/yellow LEDs on the top while the sedan ECU has it on the side...