Okay, that's interesting.... So it doesn't seem to be a low voltage condition that occurs while cranking up the 2nd engine.
As far as the RR connector goes, the yellow wires carry current from the AC magneto coil to the RR, the red wire is output current from the regulator (or rectifier, it's not clear but probably it's a RR) which eventually makes it's way to the battery charge current and the black is ground.
Personally, I prefer to disconnect the yellow wires from the RR b/c it's IMO less chance of damaging the RR. You can disconnect them all and accomplish the same goal, but the idea is to disable the charging circuit to isolate it as a potential cause. Either disconnecting the RR completely, the RR input AC(yellow wires) or the output would disable the charging circuit.
Ordinarily, both P and S engines have magneto stators with RR's, so you have to do this for both.