Slacken off the mounting bolts, run the engine and see if it makes any difference. only start the motor and blip the throttle a couple of times.
If you then carefully tighten them up it may well be that you'd somehow managed to do them up where they weren't sat right and slackening off the bolts will allow the engine to come back to where it's happy.
Failing that, put the old mounts in and see if the vibration goes. It may just be that replacing those worn components has highlighted other tired items that are now complaining cos they're operating differently to what they have for the past 5-10 years.
