I have not worked on your engine but I think this is the manual for it if you don't have it.
http://www.kohlerengines.com/engines..._32_690_01.pdf
This may not apply to your engine but on some others there is a diode in the wire between the magneto's so they don't kill each other. If that diode shorts out it will effect the operation of them. Check to see if your engine uses those and if it does you will need to use the diode function on your volt meter.
Here is the wiring diagram. It will probably not show the diodes if it uses them just like it didn't on my 3165.
https://www.cubcadet.com/en_US/conte...911d1af338c7/y