Help me diagnose electrical issue

I don't know how far discharged (low) you batteries are/ were, but running that low voltage means the charging system is lame. you seem to have improved things, but you still may have something, IE partially damaged alternator. I would start by charging batteries get them up and then see where you are.

Maybe I don't have to tell you this, but don't let your batteries sit around for a day or three "down" a ways. Keep them charged or they will sulfate, and then be reduced capacity