Right now I would say your only problem is a mis-aligned coupling. I would shim the engine mounts until the alignment is good then most likely you have eliminated the movement. Your PTO hub should still be centered OK.
I worked on a 1855 where the owner had forcibly "slugged" the PTO shaft into its final position and the result was a destroyed PTO hub. The end result was the hub being off center which really made a racket when running. I had this experience in the back of my mind when I was referring to your problem.