I've replaced the ballast resistor along with every othe component I could think of.

When replacing the ECU I checked with my meter that I had ground from the unit to the body of the car.

I have additional grouding straps from the neg. battery terminal to the body of the car, and have checked them as well.

I did try putting a jumper from the battery pos. to the coil pos. and it did not resolve the issue.
I have not tried jumping the ballast resistor yet, I could try that, along with bypassing the harness as you suggested. Couldn't hurt.