That’s a wierd one. I really don’t have much to offer without seeing the car in person, but if you bypassed the wiring to the igniter and it didn’t change, I can’t see how replacing the harness is going to help. I’ll try and find a wiring diagram and see if I can offer anything better. You may have to bite the bullet and take it to a shop however, as you have done everything I can think of from the other end of the interwebs at this point. I’ll try and poke around though.
Also, did you hear the engine run before you bought it? Did it present this problem as soon as it was swapped in? Did you use the harness from your car? And do you know if the engine did this before you bought it with the engine being bad?