without wanting to bore you all on phasing/uv joints i thought i'd write my conclusions.
having aligned the shafts by shining a torch up the swing arm I was still not happy that they were correctly aligned. I could feel vibrations through the seat and when pressing my heals into the sides of the bike. Although these vibrations were not massive it added to my woes that the shaft was not correctly aligned.
I took the swing arm off and aligned the joint so that they 100% in line/phase and then marked that position on the spline and final drive unit. I had also placed the bike in first gear to stop the drive shaft rotating. Having carefully reassembled the bike I took it for a spin and straight away new everything was as it should be
I also carried out the 30,000 mile service while i was on including the fuel filter, alternater belt, adjusted the valves to their minimum setting and balanced the throttle bodies. The bike now runs superbly. hardly any vibrations and those that you do feel are never intrusive.
for a vibe free bike line up your uv joints, minimum clearence on the valves and correct balancing of the throttle bodies.
thanks for your help guys
John