The alternator prob you are having could be fixed by just removing the caps.
(in my opinion)
caps dont work with stock alts as they discharge much faster than they charge.
Thus once you hit that big bass note and the cap dumps the alt now has to recharge the cap as well as power the system.
If the boat is not running the batteries will have to do this.
I dont think caps are a good idea.
ok Roz im ready for my education on this subject