2008 super air nautique 236. Hooked battery up backwards.

[ryansims1]

Hooked up battery backwards. I had alternator rebuilt and bench tested ok. Batteries are just fine. For some reason the alternator is not charging the system. Any suggestions?

[Beamteam]

For me it was the 100 amp in line fuse which goes from the starter to your main breaker. Easy to repair and you can bypass it in a pinch if you need to. $46 part on nautique parts.