This motor only has one powerpack. When you unplugged the one harness that has the black/yellow in it and crank the motor and it now has spark that is telling you that everything on the motor is OK. The voltage regulator has nothing to do with the ignition, the other wires on that plug in are basically for the warning system on the motor that will limit RPM in an overheat or lack of oil condition. I think if you check that black/yellow wire you will find it is going to ground. It should only be doing that with the key in the off position. Your problem could be either a bad wiring harness, bad ignition switch or a broken kill switch in the boat.
I just jumped in to help you out. If you like the answer go ahead and accept H2Os answer, so that he gets the credit for it.