I would start tracing wires starting at the kick stand switch to start and see if you can find something loose. The neutral switch is under the engine but not sure how the wires for that are run without going out to look at my bike. I don't see what he could have done from the seated position but maybe getting on or off he grabbed or like you say stepped on a wire knocking it loose. Brings me back to the kickstand switch but that alone shouldn't cause the neutral switch to stay on as far as I know.

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