Combines Standard rotor vibration

Have you tried running the separator with the rotor out of gear to see if the vibration still existsIJ

not yet. The vibration goes away as the rpms go under 600

It actually sounds like the bushings in the spline drive at the rear of the rotor are crushed sideways, at least a little, or possibly one or 2 of the bolts are bent or broken. This can throw the rotor slightly off center, but it won't be noticeable at lower RPM. Other possibilities are uneven wear on attached parts -- impellers, rotor bars, etc.