If your shifting technique is non-ideal you could be causing the clunk yourself. Modern sportbikes are designed to be raced so you should shift it like a race bike - i.e. preload the shifter, as you roll-off the throttle briefly fan the clutch and it should slide into 2nd like butter. Thats how I shift my bikes and you cant even feel anything, its like an automatic transmission.
If you are pulling in the clutch then taking your time fishing around for gears with the throttle closed you are probably wearing down the gear dogs, making it clunk more.