[Randy]

The stock civic alternator has wire to turn the voltage down to 12v... basically shut off until needed, especially with a AGM battery which has a higher discharge voltage than a flooded.

Unfortunately I don't know which wire, but it goes to the ECU, and is grounded to shut off the alternator. You can just ground it with a switch to force shutoff (the ECU controls it with an open-collector circuit). I did this when I had a '94 civic. You can even monitor if the ECU has shut off the alternator by looking at the voltage: it's about 7 volts normally (you might need a 5k ohm load or so to see this), but about 0 volts when shut off. The ECU-controlled shutoff is fairly rare: it has to be warm, with no lights or fan on.