The motor is idling at the correct timing, however it is surging every few full rotations. I have ruled out fuel issues, air leaks, compression is good, etc. so it leads me to believe it is ignition related. it has new QL78YC spark plugs, new insulated wires from CDI for that motor, new optical sensor (the one on it seemed pretty beat up. The rectifier seems fine, as the tach is stable and no erratic, the dash indicates the stator is charging and above 14 volts while running. I have two old packs, and swapped in a new CDI power pack and all three did the same thing when observing spark. The starboard bank is very clear and obvious spark jumping 7/16", but the port bank you can not make out any spark on any of the three cylinders at cranking rpm. however, fire it up and idle and all six cylinders appear to fire, and depressing the shift interrupt switch kills half the engine (so the switch is not the culprit. There are no alarms or ground outs that I have been able to find.
So my reason to think its the stator is when checking the voltage at cranking from it, the values appeared low. I checked the voltage between the brown/black and brown/white wires (one side of stator) and the brown and brown yellow wires (other half of stator. Also ohmed the wires and checked for grounding out. The ohm test was normal (560 ohms both sides) and the orange wires (50 ohms) it was the voltage values were only 75.
My assumption is that the stator is not giving off consistent voltage, which is leading to the drop in voltage and resulting in the power surge across the motor.