Monitor with your DVOM at the battery (use an extension wire to reach the console for safety) while running on the water, now that you have the fuses replaced and it appears to have been charging.
Keep in mind that the system on this engine is a MAINTAINER (it is not a battery "charger"). You really need a properly rated, wet-cell, fully-charged battery to start with. This becomes very important when you stop at your favorite fishing spot for 4 -5 hours, pumps and graphs running, etc. If you do that, it will tax the charging system heavily and take a LONG time to replenish the battery (meaning voltage may not be 13.5+ like it was earlier in the day with a fully-charged battery).
I'm not really convinced that you have an actual problem at this point...