That's a little odd, because if the stand is up and it runs, and down and it won't, then the side stand switch is working properly? For it not to start in neutral with the sidestand down the fault must be with the neutral switch as the primary condition/parameter for inhibiting starting whilst on the stand is whether or not it is in gear, which is determined by the neutral switch. In other words, the sidestand switch only comes into play if the bike is in gear. Is the neutral light behaving normally?
On a fully functioning system the clutch lever plays no part in inhibiting starting on the side stand - it simply won't do it if the bike is in gear (neutral switch closed and light illuminated.) The clutch switch only plays a part in starting in gear (sidestand up) - it won't start unless the clutch is pulled.
Either way, you can ride the bike like it is, just beware that if the sidestand switch is at fault and you ride over a bumpy ground it may cause the engine to get out. You can bypass the switch by splicing the two wires together if it becomes a problem.
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