Found myself with a couple hours spare, so I did a little trouble shooting.
Filter looks filthy, and unlike the other motor its aftermarket. So that will be going.
But I also found a couple of smallish problems.
One, the clip that secures the outer sheath of the starboard throttle cable to the engine was installed wrong and not doing its job.
Two, the block that the cables pass through to enter the engine cowling was loose, as the securing bolt was not present.
Other than that, not much.
Started each motor, ran them until they were warm, then disconnected the fuel lines and let them idle.
Both seemed to idle same speed, both were about the same temperature, measured at the thermostat housing with an IR thermometer.
In any case, I still cannot see any means by which the electronic ignition would be able to detect high temperatures and switch off.
The starboard engine very easily started multiple times, and ran like a clock ( but with less ticking noises

).
I'm going with operator error to be honest. Perhaps with a little bit of loose bolt thrown in.
I trimmed the motors in another notch while I was at it. In the really choppy stuff, there was a bit of ventilation going on.
When coming out of the hole I had to have more speed on than I wanted to have, to get the stems down into the water.
I had to go pretty quick to keep her over the hump and on the plane.
So I figured I could afford to trim her in a bit. It might slow it up a little bit, but I'm not too concerned.
In my experience on our nasty wind driven chop, it's more important to have a boat that's good at going slow, rather than able to go extra fast.
Tried measuring hertz at the primary side of the coils with my multimeter.
But looks like it's too sensitive, and every little harmonic counted as a hertz. If I was to believe the numbers, the engines were doing 24,000 rpm at idle!