Troubleshooting this kind of intermittent problem is a major pain in the butt. If you cannot see anything obvious with the wiring such as a frayed wire grounding out, loose connection or get lucky and find a defective switch I'd replace the CDI unit unless you can get a good used one to replace yours with to test.
That's assuming you actually found a good way to check the pickup coil. You mentioned that you checked it (gap) last year. Did you measure the resistance across the coil both warm and cold?
