Got a voltmeter?
Need volts of battery.
Need volts black to Green.
Need volts white to green.
With an unknown rewire, add.
Volts battery POS to Reg black.
Volts Battery NEG to vreg Green.
Repeat with lighting off.
Volts of Battery = 12.9-13V when bike is on and running
R/R Black to Ground = 12.45 IGN on.....12.65 Running ....goes up to 12.75 @ 5k....then kind of floated at 12.7
R/R White to Ground = 14mV
BATT POS to R/R Black .3V
BATT NEG to R/R Green 1.5mV
Lights were off.
Probably ok, but I asked for tests both lighting on and off to see if there were wiring connection faults that change voltage under load conditions. You drive with lighting on?
R/R white to ground at what RPM? I expected this test run with alternator not spinning. If not spinning, your regulator is sick, as the regulator should request full demand of the field coil when the alternator is not spinning.
The white to green measurement should be near battery voltage when the regulator senses a battery voltage low (which is should be with any electrical load on it).
Battery lithium? A lead acid battery needs a voltage at it's terminals higher than 12.8v in order to do any charging. (Lithium, higher V than 13V, I think).
The reg should put the white wire at full battery voltage, whenever the battery needs charge (below 13.8V for lead acid). The stock regulator pulses the white wire on a full charge battery, to average 13.8v to 14.5v at the battery. Aftermarket R/R designs may pulse or alternately provide steady V in proportion to demand. Your meter may "average" it's readings, but if it's digital sampling, there could be frequency aliasing that won't give a true reading, where it measures in the 'slots' of the pulses.
Good news is that your wiring is likely ok. But, you need to find out if the white wire measurement ever goes higher than 14mv when the battery is low and the alternator revved. If not, = bad reg.
Cheers,