Start side of ballast supplies full volts to coil when cranking engine. That wire can go direct to positive coil but hooks into wire to coil at ballast resistor. This is ignition side of ballast. Other side of ballast is supplied full volts from key. This is run position. Then it is knocked down to about 9 volts by ballast resistor. You have voltage coming from the start circuit. I believe it is supplied voltage at the starter relay when the key is turned to start. Cuts out at the run position and all other key positions. I suspect the start relay is bad. They open up easily to look for any obvious damage or maybe it's just dirty inside causing malfunction. I am no electrician but my rides all run and charge and one has a completely home brew harness as the original was to hacked up. I would open that relay up. Don't cost nothing and you might find the problem. But wasent the original problem a voltage drop? Does your battery spark when you hook up the leads? I would think your battery would drain and die from the ignition constantly on. And actually with voltage constant to the coil your engine would not shut off with the key. Like hot wiring a car. Hmmm. Intermittent short. Maybe the ignition switch.....
