So, with the bike is not running and the ignition is on the plugs and fuel pump fire some of the time? Is this right? If so, I predict the injectors are firing some of the time as well, and can be checked quickly by removing them and watching. (To avoid unforseen entertainment do not watch the injector near the spark plug you are watching.) If this is happening, there is a strong possibility that you have a short or water in the electrical connectors near your "computer" under the gas tank, or between your "computer" and your timing sensor on the front bottom of the motor. Remedy: dry out all connectors, search for worn wires.
If this is not happening, send more info. Good luck.