twin batteries cars are best serviced by replacing both batteries at the same time, If one battery has a bad cell it will kill the other battery too, also make sure the battery linking cable on the positive is in good shape as well as the grounding cables.
The alternator is a simple 2 wire type AC alternator with built in regulator, The way these are wired is that the small wire on the alternator is the sense wire and is wired up either directly or through a relay to provide full voltage, The usual fault I saw on boiled over batteries in pajero was a bad small wire on the alternator.