It's a ground or a short in one of the circuts feeding off that fuse. If possible, try disconnecting or unplugging different items one at a time, like your rear light harness or horn until the problem goes away. Another thing to do is pull one of the other 2 fuses one at a time. Obviously you cant disconect the power feed to the coils. I looked at the schematic and the wire feeding off of the main fuse goes up to your ignition switch first, this is a good place to start. You mentioned that you inspected all the wires, good, That means its more than likely a device, ie; headlight, handlebar switch. Take it one device at a time. Diconnect it, run bike for a while. ect. With intermitant electrical problems like this on a vehicle it's often vibration causing the short or ground in a wire or a device. Since I'm new at the kz650, I would wait for one of the experts here to chime in. hope this helps a little til then.