I had a problem on my 450 once, when starter motor just used too much power, leaving the voltage across battery terminals as low as 9 volts when cranking. This turned out to be below the lowest operating voltage of the ECU, and it was not working. As a result, there was no spark when cranking the engine with starter motor.
However, when cranked using the kick start, I got a good spark, and bike would start just fine.
Try hooking it up to a car battery.
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