if you have the wiring diagrams.. You can trace the injector wires from the ecu to main engine harness connector. A simple continuity test will tell you if that section is ok. Then do the same from that spot on the engine harness connector side to the injector your having the problem with. If you have continuity to it, then the wire is good.
This is how i found my problem when i first got done with my swap. Turns out during the wiring, i mixed 2 wires that controlled the #3 and #4 injectors. Swapped those 2 wires back to where they should have been, And bingo.
Just check from ecu to engine side of the bulkhead harness (where the engine harness plugs in) and from the engine harness to the injector. That'll lead you somewhere. Because this sounds like a wiring problem.. Not a component.. you proved that when you were swapping the injector connectors.