Have you tried disconnecting the stop switch, black/white wires? This can cause problems if corrosion is causing resistance instead of open in the stop/lanyard cluster. Next borrow a stock CDI and try that. Check the ground wire that goes from the stator to the E-box. If the ground is good and the stock CDI does not help, you need to get the stator checked out. The pulse or charge coil could be failing. Water in either the E-box or the stator cover is always bad, especially salt.