HC,
OK, no problem with using it to shut your bike off, in fact its a good practice.
In your original post, you said you "hold down the run button". That confused some of us, as it is a simple switch. Not something you should have to "hold down". Am I correct in saying that you just have to flip that switch and not hold it down?
Waiting for the lights to go out on thus year bike is necessary. I have the same year Road King and if I do not wait, the speedometer registers almost twice as fast as actual speed. You will notice when you turn the switch that the speedo goes to a bottomed out position for a split second.