I think you've got it!!!
Swapping the 6-pin connector swaps the ignition coils and the spark plugs.
Swapping the 4 pin connector swaps the trigger coil.
Swapping the 1-pin connectors swaps the Mag switches.
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So now we know it is NOT the Ignition (Spark) coils or the spark plugs.
Swapping the 4-pin connectors will eliminate the Trigger coils if the problem stays on "A".
Finally swapping the 1-Pin connectors should make it swap sides unless there is something magical about the switches. (Extremely unlikely but do it just to cover all remote possibilities.)
If that is the only time the problem moves that makes the Electronics module suspect number one!
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I have been thinking ... I have been told this is dangerous! (My thinking that is!)
Getting access to the stator coil to Point a timing light at them is not an easy thing to do and pointing the light at the propeller will not be informative because the prop and the crankshaft only resync once every 21 revolutions of the prop. But there is hope.
If you were to attach Two Timing lights to the engine, one to an upper plug and one to a lower plug on a single cylinder, we would expect the strobes to be firing simultaneously.
The strobed prop is going to be jumping around but you should only be seeing One prop at any location.
One degree of crankshaft rotation is approximately 1/4 of an inch of tip rotation on a 65-70" prop.
So, as long as the plugs are firing within one degree of each other you should see the strobed blades within 1/4 inch of each other.
If one spark is 22° delayed, the two blades would show an offset of 5-6 inches; about the full width of a blade.
Now that's what I call thinking out of the box!
I hope that at least sounded like English!!! 