No Case ever had the hydraulic PTO bolted to the area between the seat tower and the dash tower back in the early 70's. They were all mounted on a bracket that was bolted to the left side of the tractor behind the Operator's seat.
I am trying to understand your post. Are you able to use the tractor with no issues if the HydraCutter is removed from the tractor? It sounds to me like your vibration complaint has to do with the mower and has nothing to do with the PTO or the basic tractor.
These mowers use swinging blades that are susceptible to damage. A bent blade will cause vibration. More information please.