Misalignment of the shafts can be fixed by a flexible coupling (simple as a piece of tubing, or custom made things) or you could have a wheel on the motor and then drive the shaft or knob with it. Kind of like how the grindstone is driven by a wheel.
If you can remove vibration you can determine if it's the vibration or something else causing it.
If you can remove vibration you can determine if it's the vibration or something else causing it.