Pulled the stator cover, adjust the pick up down some to about .030. Fresh fuel, still experiencing the same symptoms.

 

A wide air gap on the trigger coil will not cause the problem you are having.

Do like toydoc recommended.  Install a new spark plug and set the spark plug gap to about .018".  If you have consistent spark but weak spark,  reducing the spark plug gap will help diagnose a weak spark problem.

If you have a weak spark (voltage to the spark plug) reducing the spark plug gap will often make the engine seem to run normal for a few minutes. 

If you have a peak voltage tester the voltage to the coil from the CDI box should be over 100 volts.  If the voltage is lower than 100v check the resistances of the ignition coil, stator source coil, reluctor (pick up coil on stator) and wires in the wiring harness.

Check all of the bullet connectors under the fuel tank.  They have a habit of getting dirty and or loose.

A bad ground could also cause the problem you are having as well as a wire in the wiring harness may only have one or two strands of wire out of twenty strands that is not broken.

I have had one LT500 flywheel that caused the engine to misfire any time the RPM was over about 4000 RPM and full throttle.  I could not detect a broken magnet, weak magnetism or any other measurable difference between the bad flywheel and the one that made the engine run perfect.