Check engine light does NOT come on when key is initially put to the "on" position?
If so, I would get that CEL light working 1st. Maybe it's unhooked or maybe you need a new bulb. Once it's working, super easy to check the codes if you go through a short sequence.
If you see burn marks on ECU board and want to get a new set up, a P06 is what I said it was (non-vtec) but a reputable company can modify it (chip it) to work well with your current B-series longblock. Its cheaper than a P28 or P72. Just make sure its for a manual transmission. If you go this route, (some new ECU) I'd get it socketed, (to hook up to a laptop) and you can have a dyno tuner modify the tune (if you make changes later).
But, once again, I'd work on electrical wiring and checking all of their work. Well.....I'd personally rip all the "tucked" out and put a D16Z6 or B18C1 engine harness. Basic-bland kinda stuff. Staying the same OBD would be my preferene.
Probably lots of wiring went behind the fenders an into the cabin....that all should be checked if multimeter dictates to check for continuity.