"or it goes in with a clunk which sounds like moving gears meshing"
are you achieving full disengagement of the clutch? Sounds like no. Yeah you mentioned "it either goes in smooth" too, but having the engine at the proper rpms will manually sinc the gears.
Try this, upshift using only a throttle cut. Clutchless speed shifting. Does it make the 'clunk which sounds like moving gears meshing' when speed shifting?
Down shifting with a throttle blip syncs the gears just fine. Not blipping sometimes are associated with louder clunks.
The reason I write this is nowhere have I read about clunky trannys and moving gears meshing in the same post.
When you are sitting at idle, in gear, with the clutch lever pulled all the way to the grip, does the bike want to roll forward?
r a m b l i n g over...