Every solid green wire (no stripe) is "ground" - the frame, engine, and battery "-" are all "ground" and there's a connection to the harness green wires somewhere. A wire terminal on a fastener into the frame.
You show a reg/rect harness of sorts but not the actual device.
The three loose wires shown connect to the bike harness, to the 3 wires that went to the OEM regulator. They are key-on power in black (all solid black wires are key on power), ground green, and field coil output white.
The plug is for the OEM rectifier. It plugs into the harness instead of that rectifier. 3 yellows (alternator output), red (to battery "+"), and green (ground/battery "-")
The other end of your harness is, I guess, the reg/rect module.
No other wiring is required. Assuming the harness hasn't been butchered of course.
The alternator output and field coil power wires connect through the engine plug. The second field coil wire has to be grounded, might be inside the engine or through that engine plug to a green wire. Both acual wires from the coil are white I believe, coil polarity doesn't matter.
One thing you can look at is the alternator wiring under the engine cover. There are bullet connectors in there that go bad partly because of the heat cycling. Also the contacts in the engine plug.