the clutch switch on most bikes is just part of a starter permission circuit, shouldn't kill the motor.

 

You say the kickstand switch has been defeated. How? Maybe there is something breaking contact in that circuit.

I had a similar problem on the KLR250 I used to have. Sometimes it would just quit, no start, let it sit for a while and it would go again. Mostly on rainy/damp days. The kickstand switch had been bypassed by using a spade push on connector as a crimp connector. I redid it by soldering the wires together. Never had the problem again.

 

kickstand wires were cut and spliced together, could be that the connection is loose. I'll try soldering instead. The bike is only doing this from time to time.