I have a 4 year old Honda 600 CBF. The motor runs fine, but every now and then, there is a racheting sound from the transmission. I've put the bike (engine stopped) on paddock stand and rotated the back wheel, and I'm getting a ticking noise. Then checked 1/2 hour later when engine has cooled and there is no noise.
When the racheting noise is there, I felt the front drive cog and I could feel the 'tick'.
Verified answer
From your information, I would suspect a bent shift fork,
Try putting it on the stand, try it in each gear, hold or tie the clutch lever down, turn the rear wheel. If you hear the tick in all but 1 gear, it is a sign of a bent fork. (For the gear it does not tick in.)
Tomcotexas.