Okay, after setting up on the centre stand I warmed the engine up then ran it up through 4000 rpm in neutral with no clunk, then did the same up through all gears with the same result. Took it for a 50 mile test run and everything appeared to be smooth, however when returning home later the distictive clunck had returned- noticable in 4th and 5th gears.
I'm wondering if it may be clutch-related, I replaced the clutch plates etc. while the bike was dismantled for the engine transplant. It changes gear smoothly enough but ......
Any further thoughts welcomed,
Ian. :dunno