With no strobe output from that lead, how would you do it?
Time for a call to Thorspark, or perhaps someone with the same system can give it a try. I thought Thorspark used a single coil with twin outputs sparking both cylinders at the same time, a so called dead spark arrangement. So maybe I'm wrong.
If you have sparks from both, it runs OK, leave it alone for now and put it down as a mystery.
RoyC fitted a Thorspark, worth an ask.
Swarfy.