Is this an aluminum boat?
If this is an aluminum boat they may have use the boat as a common ground for both batteries. Or on fiberglass may run a common ground wire. I would check the all the connections on the ground side first. I’ve found that 80% of the time when you have multiple problems that shouldn’t be related it is a ground problem. If it is an aluminum boat, I’m thinking that both grounds may run to one bolt that may not be tight or not making good connection. This could cause the starter motor to run on low voltage, and burn it up also.
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may your livewells stay full, and your rods stay bent.
Kevin