Maybe my AGMs are good enough?

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The house batteries are the only ones that should be connected to the shunt.

From the diagram it looks like you have the option of connecting the house to assist in starting the generator or the engine both having their own batteries. Always a good idea.

The shunt should go between the 3 house negatives and the boat DC ground.
I should have included the negative bus and wiring on my diagram as that would have facilitated the discussion, but it is also my understanding that the shunt should go between negative bus and the 3 house batteries, and that the house batteries are the only ones that should be connected to the shunt.

And unfortunately, I do not have the option of using the house batteries to start either the main engine or the generator. The automatic charging relays connect them for charging, but when conditions exist that would call for the house batteries to start either engine, the ACRs will disconnect the start batteries from the house bank.
 
And unfortunately, I do not have the option of using the house batteries to start either the main engine or the generator. The automatic charging relays connect them for charging, but when conditions exist that would call for the house batteries to start either engine, the ACRs will disconnect the start batteries from the house bank.
It would be easy to replace those with the Blue Seas ML ACRs that allow you to manually combine them if needed. It also has the advantage of being able to Lock-off the relay if there is a time you don't want them to combine, such as when you are doing work on the Start electrical system but don't want to have to shut down the charging loads to your house bank.
 
Actually the ACR on our generator start battery has an on, auto, off switch that allows it to be manually connected to the house bank to start the generator. Might be smart to add a switch to the ACR on the main engine battery, eh?
 

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