I'm thinking, actually, that your alternator is on its way out and is not putting out ENOUGH voltage... but a DVM would tell you for sure.
I would wholeheartedly recommend a digital voltmeter, even a $10 cheapo from Harbor Freight.
You'd watch the voltage with the motor off, with the motor cranking, and if it runs, at running.
With the motor off you should see a smidge over 12V; even cranking it shouldn't go below 10V at lowest... and then running, you should see 12.5 to 13, maybe 13.5 tops. More than that, your alternator is on the fritz and you're gonna fry coils along with whatever else. Less than that, the alternator isn't doing its job and is undercharging.
You should also check voltages around the system, i.e. at the batteries, at the alternator (red lead on the output, black lead on various grounds), etc. If you get wildly different voltages with different grounds, then you can chase down those grounds as suspect. If you get wildly different voltages at the batteries than at the alternator output, then the isolator is suspect, etc.
If it's a diode-based isolator, you should see about half a volt difference from one side to the other; if it's relay-based, then you should see no material difference.
Hope this helps ... it's a start, as it were =))
-- A