Just been over the wiring diagram. If the P.O. just shorted out the side stand switch, the power still goes to the side stand relay. In effect, all he's done is put the relay directly to earth, rather than the side stand switch closing and putting the relay to earth (i.e. completing the relay circuit to earth) In the diagram, to the left of the relay, you'll see a pair of diodes paired to a central point. One diode lets current flow from the relay to the neutral indicator light switch, and the other one lets current flow from the neutral light to the neutral indicator light switch. They're there to stop cross feeds. Looks like the P.O. only did half the job. Starting to look like the problem lies in the actual side stand relay itself. Check this out and let us know.
Trying to explain a bit more, the neutral indicator light switch closes when you're in neutral, allowing power to flow from a +ve source to the neutral light, then via one of the diodes to the switch, which closes to -ve, thus completing the bulb circuit, and allowing it light up.
Power goes from fuse #3 directly to the side stand relay, but now, with the side stand switch effectively shorted out, the relay is permanently energised, with a diode going directly to the common point of the diodes to the neutral indicator light switch.
Like I said - definitely looking like a side stand relay problem.
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