I had an issue that was similar to this one a while back....my keyswitch had a short in one of the wires causing it to work sporadically. I went through checking my stator, coil, CDI, and proceeded to the wiring and that's when I found it. I bypassed the keyswitch and bam, problem solved. When you get the chance, trace your entire harness and look for any pinched or broken wires. Insulation may have worn off a critical wire and it's grounding itself out on the frame or something...Make sure all connections to your coil and CDI are snug, maybe something rattled loose I can't imagine it being anything too major, it's just finding it that can be the PITA