I had a similar problem with the external alternator. It wasn’t diodes or a wiring issue and took me months to figure out. The 12 volt wire that energized the alternator has a plastic clip retaining it to the alternator. Vibration was causing it to break contact. I removed the plastic housing, installed a new bare metal spade connector and bedded it in RTV. That was over a year ago and it charges at 13.9 volts all the time now. Hope this helps.
Ed