If everything is in line you have changed the b/box mount and you are sure as the clutch is good then I would look for a worn engine mount.If the box is making contact to the body its got to be moving somewhere.I say this as I had it with a Manta (lol) years ago.It would only move enough for the box to touch just on pull off between say 2/3 thousand revs.

Also had a slight judder when a couple of gear box bolts worked slightly loose on a mk1.Its worth checking.