I guess all blacks end up at the same place in the end. That's ignoring the ignition black on magneto models though.
What type of regulator have you bought as 'i think' they just earth out to wherever you screw them to the frame [unless remotely mounted to plastic somewhere but heat might be a worry on plastic--what's that dripping!!].
Reg's i'm thinking just have a yellow wire. But in saying 'that' original non finned ones might be mounted under the airbox so an earth from the Reg body mount bolts to earth somewhere frame or loom.

I have it temp mounted to the bottom triple tree fender mount holes 

Yep, so best earthed as you want to as bit dodgy earthing through moving parts [steering head bearing].

After i get it started , I wondering about doing a volt test to see if the voltage regulator is doing it's job before I plug in the headlight

"Also, the male black bullet on the headlight plug , am I correct to assume it would plug into the black triple female from the main harness , essentially giving more places to plug in black grounds?"

That is what I have done.

As RT325 says, the earth black wires all feed back to the negative terminal on the battery.

If you had the components (voltmeter, couple of wires and spade terminals), you could rig up a test unit and see what voltage is being sent to the headlight socket.

Why not just mark the flywheel and crankcase, so marks align at the firing point, and then strobe the timing?