I have been playing around with the schematic tonight and trying to figure out how the coil and dash are related.
Interestingly enough, the dash unit is largely responsible for controlling the exhaust valve. There are 5 of the 16 pins dedicated to powering it, and knowing where it is at all times. Then, 3 pins are for turn signals and brake lights. 1 for the fan, 1 for the key sensor, 1 for the fuel level sensor (which interestingly is a variable - I wonder if we could get a fuel level gauge from it rather than just on/off). I think we can rule all of these out as factors.
This leaves us basically with power, ground, and the CAN communication pair from the ECU, which is basically a serial communication.
Then we have the coil, which has 3 wires.
We have the power, the energy behind the coil that allows it to make a spark, the trigger signal from the ECU to make it spark, and the signal ground. The spark is grounded through the engine.
So.... important question. Has anyone had this exact problem, and been successful in replacing ONLY the dash unit and coils (not the ECU)? If so, we can at least narrow it down.
As for preventive measures... my only thought is to install something in-line with the coil that will prevent voltages higher than ~40V from backfeeding into the rest of the bike. Maybe it would make the bike stop working, but it would protect the dash and ecu...?