I think the ground for the Voltage Regulator would only matter to the lighting circuit, not the ignition.
The gray and black wires at the 1st Engine Connector coming from the CDI.....all they have to do is touch together and the engine should shut off. That is what the key switch or the kill switch does, in the off position...it simply connects the black ignition wire to the gray ground wire to ground out the ignition.
If the connections are all good, what about the ground point shown on the wiring diagram just below the CDI....and the Ground for the CDI itself?
Lastly, if that is all good, one of those wires could be broken inside the insulation....Or...it's pretty rare, the CDI may have failed internally and will not shut off the ignition..? Some Arctic Cats with Suzuki engines had that problem with their CDI's.