Here are a few more places to look...

How do your isolation & tie down pads look?
Is there any debris between the bed plate and machine beam?
Are the bolts to the tie downs & isolation pads installed correctly?
If you back off spring tension one roller at at time on the rail guides is there any change?
Did you change the ropes?
Is the vibration different in opposite directions?
Are the new compensation chain the same weight as the old chains?

Also, Can you post a picture of the motor mounted to the machine?