There would certainly appear to be an intermittent short in the system somewhere, so it should only be a matter checking through the wiring carefully, however if it only occurs when the engine is running or the bike is moving or vibrating then it does become more difficult.
You could try fitting some temporary lower Amp fuses (10A) to each individual circuit (ignition, headlamp, brake light etc.) as that may help you to pinpoint the actual circuit that has the short as only the lower rated fuse on the affected circuit should blow.