The rotor on the DOHC is famous for testing as good all day long then not being so. They short internally and can charge at lower rpm but put bike out on the highway at steady higher rpm and then it does not, centrifugal force makes the wires then short to not charge as much. Slow back down and suddenly you have full charging again and it can show up on even new rotors. It does not happen on the SOHC because that field setup does not spin at max rpm like the DOHC does, it is fixed in place. Even a light drop of the DOHC on the right side can make it do that too, the rotors are really easy to break, I've had 3 on mine. The last one did just what I said, bike stayed charged up in city and then the problem only showed at steady state over 5500 rpm, the battery would then run down. Battery stayed up forever simply sitting.
So, if any of that sounds familiar you have an angle to pursue.