Here is an update. I just got my ACU back from Tony. He said there were numerous spikes to my ACU and they caused some faults in the program. Those faults in the program may be responsible for the surging and other running issue. the errors in the program directly relate to the RPM's that I experienced the problems. So at least that is taken care of. And the rest of my problems should go away with the replacement of that bad stator. I pulled the bad wire to the side and can clearly see where a wire is burned fast to the bare copper coils of the stator.
So anyone out there with an intermittent problem it pays to search and take thing apart to actually get a look at your parts. Thankfully this was easy to spot from looking up under th flywheel.