To check source of vibration, I'd suggest first operating the separator with the rotor out of gear. If you have vibration, it's likely the chopper. Suggest that you also loosen the peripheral drive belt idler (drives chopper and shoe) on the R_H side of the machine and re-engage the rotor to check for vibration there, as well. Have the bolt holes in the crossmember become oval from the vibration and operating while bolts were looseIJ If so, it's likely that you won't quite achieve proper alignment again and probably need to replace the crossmember. Although the bearing floats in the flange, it's still critical that centering is as close as possible. Hope this makes some sense.