The Hall Effect sensor in the 'bean can', may be something to think about .
But that's the problem with electrical parts, on average, they give no warning before failing .
You stated that you have two ignition coils, from a production date of 09/80, until the end of the airhead series bikes, sometime in '95, they came form the factory with a single dual output ignition coil .
Sounds like you may have a previous owner 'modification', due to the cost of an OEM replacement coil .
A couple of modifications that I have made to my R65's, is to relocate the negative battery cable from the transmission vent bolt, to the lower right engine to transmission bolt, with a replacement cable form a chain type auto parts store .
The other was to make up a larger diameter ground, or earthing wire from the main grounding, or earthing point at the voltage regulator where all of the bikes individual systems come together, (at least, on the twin shock bikes ), I made up a wire that goes from the main ground point, to the negative post of the battery .
When you replaced the ignition control module under the tank, did you apply heat-sink compound to the mating surface between the module and the aluminum heat-sink ?
Or was yours one of the module bonded to the heat-sink type ?