9V issue is likely my issue. Checked it again today, took 3 readings, and it is 11.3 V, slightly lower than the reading at the battery of 11.7 when the key is on. I recleaned things along way, anything I removed got a surface cleaning, including bolts and where they went into the frame. Hondaman has pointed out that these can cause issues if the ground to frame becomes dirty.
Ran it out on 20 mile ride each way, outbound was no headlight, voltage at battery after letting it settle was 12.65v.
Ran it back with headlight back on, voltage at Battery was 12.5V.
It seems to be working for now at least, I will have to keep an eye on it.