In a wiring diagram, it shows how the wiring goes from an electrical point of view, not the Physical view point. So what a diagram shows is not exactly what it looks like on the bike.
Just follow the wire colors and you will be fine.
The six wire plug usually has the three whites, the green and brown wires from the stator and brushes, it also has the blue wire from the neutral switch in there too. The only other wire near there is the yellow wire, it come up from the stator and is in a single plug that goes to the safety relay, if no SR then it gets capped off.
The brushes are the green and brown in the 6 wire plug.
To get the alternator to function you just hook up the three whites from the stator to the three whites of the reg/rec, the brown wire from the brushes to power after the main switch, the green to the green on the reg/rec. The other wires on the reg/rec the brown to power after the switch, the red to battery positive the black to battery negitive.
Just as the diagram shows.
Your bike won't run well or long without a good battery and working charging system. so get it right first, then add the ignition to get it to run, then once running add the lighting.
Leo