Testing both ignitions is your means of checking both work then, that sounds acceptable, you wouldnt know if one failed during flight, but you'd notice at the next pre flight check so that might be Ok for a small craft.
Yes you might be able to use a cop system, there are 2 things to consider, there is some 'smart' circuitry in these, there might well be some voltage measuring circuitry meaning if you dont have a charging system they might not work properly due to the power supply being <13.8v.
Secondly and more complex is these units tend to be constant energy spark coils, meaning that the trigger pulse supplied needs to be a constant length irrespective of engine speed, so you need a processor to calculate when to fire the coil and provide the same length trigger pulse independent of crank Rpm.
The existing low voltage coils could be used you are correct, probably the best thing to do is process the signal from these using a dedicated pickup coil amplifier ic.
You might be able to get the whole lot working with an arduino, or 2 for redundancy, you might need a leonardo to get enough speed depending on max crank rpm, I'm guessing a smaller motor might well get to screaming revs.
The 4th wire on a toyota cop is a signal back to the ecu to tell it that the spark was actually successful, if there was no spark then there would be no pulse, you could use this for a on board diagnostic system to detect a fouled plug/broken lead/other fault.
Other systems might have a different function.