Replacing the Alternator
Before I started our trip to Alaska this spring, I replaced the original 83 amp alternator on a Perkins 6.354 with a Balmar 100 amp with a separate charge controller. The first alternator "ate itself" and is back at Balmar being "evaluated". The second one works as planned. In the course of replacing it, I also replaced an old West Marine ACR with a Blue Sea ACR. During the installation, both the instructions and local marine installer recommended connecting the charge controller sense wire to the house bank, since that was the bank with the most charge demands. I did that and things worked fine until about day 3 in our trip, when the charge voltage jumped up to 15.9 volts on initial startup and the ACR refused to combine the house and start banks (It won't work above 15.6 volts.) I shut things down and did a quick inspection and fired things up and everything worked correctly. The same thing happened two days later. At that point, I decided the problem was the sensing wire looking at the voltage on the house bank and the charge controller wanting to throw everything at the house bank even though the ACR had not combined the house and start banks. The voltage escalated up to 15.9 volts because no matter what the controller did, it didn't see a change on the house bank voltage as the ACR hadn't switched yet. I moved the sense wire over to start bank and everything has worked as you would expect for the last 18 days. The only thing I have noticed on a couple of occasions in this configuration is the alternator won't initially output anything until there is a sufficient voltage drop on start battery to trigger charging. This generally occurs after running for a long period bringing all battery banks up to 100% and then shutting down for fueling and then starting back up.
Hope someone can use this experience.