Well, for sure the clutch switch is out in the funk and benefits from a periodic clean, dielectric grease and seal.
Just from the wirng diagram, it routes power from the start button to the starter relay to engage the starter solenoid.
There are three points of concern in the run circuit :
1) The power to the ECU/FI relays goes through a single connector located under the relay stack. While it is a weather tight AMP connector, it does sit just above the rear fender and will benefit from a clean, inspect, dielectric grease. afterall, all the power to run must go through it.
2) When in neutral, the power to the run switch is through the middle (neutral) relay referred to as the " safety relay for stand " in the manual. It is not activated by the side stand but by the neutral switch. The neutral switch is prone to sticking ( always park in gear) but will not interupt running, just that the neutral indicator light will stick on.
3) When in gear the power to the run switch is through the side stand switch situated on the leading end of the side stand. This switch is really down in the muck! And all the power to the run switch goes through it. Periodically inspect ( along with the wires which run along side the alternator cover), clean with a spray contact cleaner and force in dielectric grease.
If power to the run switch is impeded through the side stand switch , shift into neutral to see if normal running is restored as the 'neutral relay' provides an alternate route for power to the run switch .
Keep the smoke in the wires!