the regulator is only for auxiliary circuits (lights) it has no effect on the coil and can be left in the harness and plugged into when you want to use lights by just simply unplug the connector at the stock light switch location in harness and use the yellow wire to feed a toggle or any switching means and run lights as long as they are not above around 65 to 70 watts...
but yes it would be good to insulate the live end when not in use
in the stock stator you can see there are 2 distinctly different sets of windings one set for the cdi to coil for high voltage spark,, and the others are for lights and what ever you want to setup if clever ...but 2 separate sources completely ... you can just about fry your stator lighting coils and still not change the way the quad runs