Get a accurate cheap voltage meter. I think your battery is running way down in power. Check the voltage with the ignition key in the RUN position.
Do you have enough electrical experience to do the voltage check ? If not ? you can damage things. Including yourself.
With both the main and the kicker motor doing the same thing ? If you have electrical fuel pumps ? Battery voltage can affect both motor. Get a marine mechanic who does Yamaha motors. Good luck.