My first thought is that you have wiring or injector problems but you say you've checked those circuits. Assuming everything is actually good, you're back to the ECU.
You say you had the immobilizer removed, how did you do that? I assume you had someone modify the ECU software? The software would be a common denominator and something I'd be looking at.
I'm curious why you're putting this much time into using a stock ECU in a non-stock application? An aftermarket controller may be easier to work with.
Last but not least, hello from a fellow instrumentation guy!