The Upper Bearing and Cup live just below the upper rotor head. It's the bearing at the TOP of the outer shaft. The inner shaft runs through the bearing. If the cup isn't seated squarely on the top of the outer shaft, the inner shaft will wobble. And if the outer shaft is bent a bit, it will cause the inner shaft to wobble. And if the very top of the inner shaft is bent, the shaft will appear to roll true on glass, but that little bit of inner shaft that fits into the head can be bent and that will make just the head wobble.

Finding shakes and vibrations is a curious endeavor. It will cause you to learn the relationships of many of the parts in the helicopter. If you have to dig deep, just go for it. Don't be afraid to pull the entire drive system apart and put it back together one piece at a time. Be certain that each component you install is correct. I can tell by the way you write that you have your wits about you and you'll likely find this to be more of a challenge than a frustration.

The Static Balance that is done when you balance the blades on two edges is just that. Static. It is certainly critical, but it's not all-telling. Dynamic is the balance that results in flight vibration and it is driven partially by the static balance. The rest of the dynamic balance is the result of the 'aero' dynamics of the blades. Each pair, upper and lower, must track correctly or you will have more noise, less power, less battery life, less lift and more vibration.

Keep after it and let us know what you find. Oh, and loose body parts can amplify the look of a vibration.

Have fun!
Soloboss