If there are two trigger coils triggering two ignition coils that each fire two plugs, why would a trigger coil only cause one plug to misfire?It's only one cylinder doing it, it's not your wire/cap combo.
If it does it on the same cylinder with 2 different sets of coils, I'd take a close look at the triggers. I didnt read enough to see whether or not you have points or pickups, but it doesn't matter. If you have points, I'm sure you have set dwell and gap plenty of times, tried new ones, etc. If you have dyna or another ignition with pickups test the A/C voltage while cranking on both pickups.