I think barring a miracle discovery you're going to have to sort this out one item at a time. I already know you're running a pretty stripped down scoot so extra power draw isn't going to be it. A good look through the headlight bucket to eliminate any bare/exposed wires would be a fine start. No joy?
Then here's my idea: with the bike off and the key removed pull the ground wire and put your meter in series with it and the battery so you see the voltage draw. Engage the kill switch and see if that really has an effect. Then systematically pull one fuse at a time (then replace it) until the meter reads zero to locate the faulty circuit. It is remotely possible that the terminal that feeds the kill switch in the ignition switch is faulty while the other terminals that feed the lights, etc. are good; having the meter drop to zero when fuse #2 is pulled might, just might prove that.
