What you describe - lights from the alternator only - was common on 2-strokes with magneto ignition, a generator/alternator powered the lights so you had no lights unless the engine was running. The Honda 400-4 does not work that way. The entire bike runs off the battery, and the alternator is connected to charge the battery and, of course, it powers the bike as well when running while any excess power charges the battery. Once the battery is fully charged the regulator controls alternator output so it just makes enough power to run the bike without overcharging the battery. In actual riding, the battery is discharging if below around 3000RPM as alternator max output at low RPM is less than the combined ignition, regulator, and lighting load.