The auto tranny and 5 spd ECUs are not interchangeable if for nothing else than the fact that the two cars use different sized injectors (450cc for 5 spd, 390 for auto). The 90 ECU also differes from the 91-94. See
www.vfaq.com for the differences, I believe you can swap two wires on the harness to make it work. The problem as you describe it does seem to be the ECU, and it is common for 1g ECUs to shit the bed, especially the early ones. All you 1g guys should be replaceing your caps, or having it done
Again, see the vfaqs for more info on that.