Remember, K.I.S.S. (KeepItSimpleSir)
You're only dealing with four wires exiting box for the switch. One issue I have with my diagram getting circulated on multiple forums, sites and on Facebook over the past years, is guys don't know the post (my hx1100) it originated from. I suggested ALL the factory connectors/plugs inside the ebox be cut an removed. Not only does it make it worlds easier to figure out what goes where, what gets cut and what gets spliced, it alleviates the possible failure at the old connections. 9 out of 10 may "look" good, but they have bitten many guys in the rear end, as the prong was the weak point inside the connector. My diagram also doesn't show the wires associated with the stator or coil wire colors... that should be a no brainier as to not be cut/spliced/removed!.... or so I thought.
YES, my diagram has been questioned when guys have had issues, but only for them to eat crow when I showed what they did wrong!
The ebox can appear to be a rats nest for some who have never done it before, but luckily I'm only a PM away if there's a question.
Kawasaki colors from ebox TO Yamaha switch are :
Yellow w/red - Brown
Red - Red
White - White
Black - Black
Your box should work WITHOUT a secondary ground. I would suggest unplugging the four prong blue plug at the regulator/rectifier, and check your black wire(s) at that prong for being broken.