Running Voltage Too Low, Now Too High

Found someone with a similar issue on a different bike: https://www.reddit.com/r/Fixxit/comments/38mv11/2008_fjr1300_my_fjr_is_intermittently_deciding_to/

It sounds like their problem was bad grounding but unfortunately their solution was to take it in for repair. At least it gives me a good idea of what I should be looking for.

 

The slightly high voltage I would check this again. Measure the voltage at the Brown and Red wire on the regulator connector, and IMHO there are likely quite a few XJ's running around with close to 15V.

The flickering low beam light seems to be occurring right at the point where the AC Generator is providing all the power and beginning to charge the battery. I am not sure that means much but I would try a different bulb as the xenon bulb may not be compatible or is more sensitive to the AC component of the AC generator.

Does the high beam flicker like the low beam when selected?

With low beam selected probe the black return line at the headlight H4 connector in reference to battery negative. You would need to see at least 2 to 3 volts for the high beam indicator bulb to be visible. If you see the 2 to 3 volts then either the ground is inadequate or there is excessive current (xenon bulb).