Grab the part number from the ecu casing and that will tell you if its an early or late gen 2.
Have you tried pulling fault codes from the ecu? Hopefully whoever did the engine conversion connected up the ecu fault light on the dash (which flashes the codes)
Might be worth going straight to an ecu swap out as you suggested if you can borrow one locally or from on here.
I wonder if the injector resistor pack is okay? The Big Green Book has tests in it to confirm its good from memory.