I would trace all the wires coming off the batteries. Besides knowing where they go and what for, the wiring at the batteries is a puzzle to me. On the one hand the batteries are wired in parallel to maximize the amp hours available (parallel), yet the are also pos wires coming off each pos post and heading off into the boat and the same for the negative wires- this makes it look like the batteries are being used individually (all depending on which red matches up with which black wire). This may negate the paralleling of the batteries...