Just at first glance from your photos, it looks like the frame was not properly masked at the main mounting points for the engine. If that is the case, it is probably worse at the transmission cradle which must have not only been masked at the bolt holes, but also the outer 1/8" of the main isolastic mount tube (same for the front mount), as well as the flats where the swingarm bushing faces slide in place...
I hope I'm just seeing things that are not there; if not, you have a few hours with a dremel burr and some sandpaper in your future!
author "Old Bikes"
too many bikes to list, including:
JPN, 952 Prototype, MkIII Interstate, Combat Dunstall, VR880 SS, Triton