In my case, we determined that one or both mags were not able to handle high RPM (over about 4K) once warm. It was intermittent and became worse over time. Replacing the modules resolved everything. Honestly, if you already have any issues with one or both modules, replacing both would seem to make sense.
Interesting though - did you mention that the engine won't shut down when mags are shut off? I'm sure you've checked your plugs for carbon hot-spots, so . . . something to check that would be cheap and could be related: I would want to check for proper grounding from modules through mag switch (or ignition switch if integrated). Check resistance to ground for each mag when switch is on and off -- should be no resistance one way and infinite the other. That's me thinking out loud - not sure if this is solid information.
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