realy nice work, but it looks like an little electrical problem now...
1. is the engine running, if you kick it ??
2. i think maybe you only need isolation between the voltage of the e-start-system and the ignition-system , that the e-start-voltage can not bother the performance of the ignition-system, if you try to e-start the engine.
some years ago had one of my riding buddys the same problem with his ktm 300 exc, kickstarted it, runs... than try to e-start: no spark!!
kicked it again, sparked and was running with the same sparkplug.
he went with the bike to the local ktm-shop and they solved the problem with better isolation, that the voltage of the e-start-system cant touch the engine-cases and only works between battery and e-start-motor as an closed system, because the ignition also use the engine housing to work as an electric circle. any external voltage will bother it and the spark could be completely gone or simply not strong enough to ignite .
my idea is, that you should install an isolating gasket to the ignition cover and isolating washers between cover and bolts, that no e-start voltage could reach the ignition system...
... its worth a try !!
sometimes is the problem much smaller as it looks in first...