Joe,
To be properly synced all of the carb adjustments must be the same. The slides need to rest at the same height, be at the same height at wide open throttle and begin to raise at the same time. The pilot air screws must be the same amount of turn out from bottom and all of the jetting specs must be the same. Check the spark plug caps, make sure they have a good tight connection to the plug wires. The pickup coil gap should be .018"-.020" measured between the pickup lugs on the flywheel and pickup coil, if one lug measures differently from the other it would indicate the crank being out of true. Also it may be a good idea to check the compression, a cylinder with low compression may not fire in the lower rpms, then will begin to fire as the revs increase. Hope this all helps.