First of all, the ECU's rarely go bad on these cars so I would rule that out without checking the sensors first.
By looking at your info your from fullerton which means california and an M/T means you don't want to put an auto ecu on there without mods.
California has an extra oxygen sensor on the cat I beleive so you have either a modded exhaust and disconnected the sensor and the UCU isn't getting feedback from the oxy sensor or its bad and your ECU is sensing this.
I don't know the subtleties between the different ECU's
except the color of the plugs on 86.5-88 are yellow and 89-92 are grey.
It is possible that the one you put in is 89 or later and causing it to run bad. Check if the plugs are grey and try plugging in the yellow plugged one from a 86.5 -88 M/T, clear the codes and see if they come back and see if the idle smooths out.
I'm not sure if there was a special ECU just for california or not.
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