Thanks for all your advice. It would seem there are many possible solutions depending on all the variables, both human and mechanical, at play here. I shall be fitting my ECM back this weekend with the new TTP tune in it and, from what I've read, hope that this should change things enough to make a difference to the vibe problem as well as all the other benefits I'm expecting. I'm afraid Mike that I'm not capable/proficient to do the checks you suggest and shall have to rely on your good work in the tunes you've created.
Whatever the result I shall certainly give feedback on the effect these upgrades have on my bike. Good vibes ahead hopefully!