Well it would be a place to start trouble shooting. It would be best to use the ECU, engine and tranny (especially an auto) from the same year. I'd look into whether or not anything changed from 87 to 89. If nothing else maybe a sensor or wiring change.

93 4X4 ext-cab, auto, SR5, 3.4 V6, supercharged, 2.1" pulley, URD fuel mods, Aquamist WI, IPT valve body mod, dual cases, 4" superlift, Alcan springs, 33 BFG MT, ARB locked front & rear, 5.29 US Gears, RB 1" BL, 1.5" BJ spacers, TJM T-17, Warn m8000.