Have you done some basic checks on the suspension and bearings at the rear end? Bounce the back end and see if the compression and rebound damping is still there - easier to see the rebound damping than compression, and make sure you cannot move the wheel in directions it is not meant to move in. I had an ST2 with 16k miles on it and the rear wheel bearings were shot - I could hold the trye and move the wheel from side to side. The problem was the bearing was exposed to the elements so it suffered. Is the 749/999 like that too? Reckon it might be.
Oh, and one other thing. You haven't got an Ohlins with the remote preload adjsuter like on the ST4s have you? One of my "mates" thought it funny to twiddle with that and screwd it up tight. That turned the rear suspension into a solid bar. I didn't see the funny side, funnily enough
