Thanks for all the replies and interest given to this thread.
Did the thumb test and the carbs are fine. I went down one on the pilot jet and it ran worse so I quickly changed it back. The pilot screws are now three and a half turns out. Still, it runs great with absolutely no hesitation while under power. Just trying to cruise at any speed and it will seem to surge or slightly buck, not sure how to accurately describe it. The pick-up coil is new from the factory and the timing advancer seemed to work fine when I put it back in after the rebuild. Simply at a loss what to do here. So much time and money spent on this project.