Originally Posted by captbillc
i expect the voltage will not rise for a while because the batteries were so low.
I often find quite the opposite: that discharged batteries will accept a charge quickly and have a higher voltage (12.5-12.7) and then discharge quickly (self-discharge back down to 12.0-12.1 in a couple of days), due to the initial charge only affecting the outermost layers of the plates.
The part I don't understand is
I'm getting 13.8 volts at the alternator. The alternator output wire joins the harness and travels back to the cockpit engine panel. When I read the voltage there it's 13.2.
I've tested the output wire for resistance and got a zero reading.
Do you mean that the wire from the alternator to the cockpit engine panel has zero resistance? How exactly are you getting these readings? If there really is a voltage drop in the wire, then the wire must have a pretty nontrivial resistance.
Is the wire disconnected at both ends when you check for resistance? Are you using the same ground when checking for voltage at the alternator output and at the cockpit engine panel?