Thanks, Maine.. when you say 'lose the isolater'... do I replace it with something else? Actually in light of all this I'm considering tossing the mess and starting over with a Balmar/equiv alternator too.....
You can replace it with a Balmar Duo Charge, Automatic Combining Relay, Echo Charger or one of the Sterling battery to battery chargers.
When you do any of these upgrades;
run the alt output B+ direct to the house bank
run the MC-614 voltage sense wire direct to the house bank
Use the same sized neg wire for the alt as you have for pos and make sure it too has clean connections back to the house bank. (preferably NOT though the engine block)
insert a Duo, Echo or ACR between the house and start banks and let it take care of the start battery.
Install fusing for the alternator output and sense wire within 7" of the house bank + terminal.
It is a good idea to fit a "service disconnect" for the alt output in the engine room so when working on the engine the alt is not live.
make sure that shunt is robust enough for the output of that alt and those connections are good and clean. Any shunt in the + wiring should be 100% protected from shorts by means of covering it. This is why most battery monitor shunts are installed in the neg lead not the pos..
If you have a battery monitor you could also get rid of the alt shunt and ammeter.