I read on here that the APB and BELs ECUs are not compatible, to the point where you would damage either one if you attempted to plug it into the wrong harness.

So I made a comparison of the wiring for each ECU type as an attempt to find out why this is.  For the most part, they are the same with a few wires swapped around.  A few of those may be due to the different MAFs (Bosch vs. Hitachi).  As far as cause of failures go, it looks like there may be a switched power on the BEL that goes to an unidentified spot on the APB ECU (pin 15) and a constant power in the wrong spot (pin 30).  Maybe this is what is frying the APB ECU when you plug it into a BEL car?

In any case, please review the spreadsheet below and let me know what your thoughts are.

If it helps, the APB hitachi ECU has the same pinout (as far as I know) as the bosch APB ECU

Could the fact that the BEL does not have ignition modules be causing the problem?

APB has two ignition modules (bank1 & bank2) and coilpacks.

BEL is wired direct to coilpacks.

I'm pretty sure that's the only difference in engine wiring loom between the two engines.