When it is acting up unplug the regulator. If it quits charging could be the regulator. I have seen two things happen at the alternator. One the regulated to ground brush terminal or insulators failed and grounded to the case causing full fielding and two shorted to ground armature or slip rings again causing full fielding and overcharging. Even though the harness is new if the regulator 12 volt feed connection is poor or bad the regulator looses voltage sense and reacts by trying to charge what it thinks is a low or dead battery.