Battery Kill/Disconnect Switch problem/replacement

^^I was going to post that. If you run the main output from the alternator through the secondary contacts some?/ many?/ most? switches are not intended for that.

If you use a 3 wire alternator, use the second contacts to break the ignition and field wiring through a relay. You can also break the pump relay circuit if it is separate.

So far as protecting the alternator (from spikes and surge) there are various "load dump relays" in the marine industry but I have not researched them.