Hi Graeme — some other suggestions:
1. Are you sure that the isolastics are adjusted properly? Some go by the book, set the clearance with the feeler gauge and then torque the engine bolt. This can be a mistake because the slack in the threads is taken up and the clearance is effectively reduced to zero when the nut is tightened. On mine, I have to back off the adjusting ring more, tighten up, then check, and repeat till I get the 8 thou I want when everything is nipped up. Please ignore if you already know this.
2. Slacken the isos off quite a bit. With the bike off the stand, grab hold of one header pipe and see if the engine moves in the front mount. Grab the rear wheel and you should get plenty of movement and you should even see the front of the engine moving (if you have the standard head steady). Then you know that the isos are responsive to adjustment. If you don't get any movement, then something is binding/stuck/bent, etc. and the isos are not functioning as they should. While everything is slack you might also be able to hear/feel if the engine/gearbox assembly is hitting the chassis where it shouldn't. Then, adjust them back to the 8-10 thou as per my method in 1. above.
2. Try removing the head steady, take the bike off the centre stand and rev it through the normal rev range and see if it makes a difference. You might also hear/feel if something is touching the engine, as has been suggested in previous posts. I agree that the left hand zorst can touch the frame, causing excessive noise and perhaps more vibes.
3. When you fitted the new isos, were the engine bolts a snug fit in the tubes to which the rubbers are bonded? Some of us have had unhappy experiences with sloppy fits in new iso parts. It's a long shot, though.
I am assuming that the isos have been properly assembled with the right sequence of parts in each assembly.
Please let us know what you discover so as to add to our knowledge bank!
Dave