The process would go like this:
1. test waveforms coming out of flywheel triggers at connector
2. verify same waveforms arrive at igniter-box connector
3. test ignition-triggers coming out of igniter
4. verify same waveforms arrive at each igntion coil
This will tell you if it's a flywheel-sensor issue, or igniter problem or ignition-coil or wiring in between with exact 100% precision and certainty. Baring that, you have serious wiring issues, so I'd just get a replacement harness that hasn't been all hacked up and put back together. I suspect you have a short in ignition circuit which can fry the igniter. Check out this similar thread:
2010 only running on one cylinder.