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Home Port: Lake Michigan
Vessel Info: 52 Sovran, Cat 3406
May seem obvious but I assume you verified that the alternator is in fact over-charging by using a digital volt meter on one of the battery posts? Wouldn't be the first time a gauge put out faulty information.
I am a little hesitant to offer too much advice here without seeing a diagram or knowing the configuration of the alternator. But yes if your problem alternator is connected to the isolator, removing and insulating (very important) the common lead (red wire from alternator) should prevent that alternator from outputting anything.
Safer option is probably to just remove the belt. Or if you are able to get to the small gage wires going into the regulator, disconnecting the excitation wire (usually purple) that connects to the key switch will prevent the alternator from generating any current. There is usually a barrel connector on this lead.
The other small gage wire is the battery sense wire. When troubleshooting check voltage here. A bad connection between this terminal and the battery bank will result in the alternator putting out full charge.
Good luck and remember to cap off/insulate any open wires to prevent a short. Also good practice to disconnect battery grounds prior to messing around with any wiring.
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Home Port: Holland, Mi on the Great Lakes
Vessel Info: Tiara 1994 31 Open w/ 7.4 Crusader Engines
Thank you Admiral for your response. Yes, I did make sure I tested at the battery. It was actually putting out 64 volts. I am lucky that it doesn't appear I fried anything. I disconnected the red wire at the isolator and sure enough the alternator isn't charging anything. As it turns out I will be replacing both alternator's since the other looks just as old.
Again, thank you for your help. I'm sure I will need more as I continue bringing back this beautiful Tiara.
Holts13