To test;
Get the bike when cold, make sure starts & runs Ok but dont warm up. Isolate CDI box away from bike & heat with a hair drier, (Or a heat gun but only on low) & when nice and WARM put back to whenst it came, start again & go for a ride. Rest of bike should still be cold so if breaking down happens sooner than before it could be your problem. If not, & you want to try first if you think it's pulser/charge related, heat up the flywheel area, it should be able to get WARM/HOT as per normal & repeat ride. Dont forget though, high tension coils (Spark plug coil) can & do break down when hot.
Viper666