Take a look here in the self help section, see if anything here applies.
Transmission,Clutch and Primary (Drive Train)
Transmission,Clutch and Primary (Drive Train)
To follow up on TQ's post, sounds travel. I recently changed out the cam chains on my scoot, I would have bet big money the noise/clicking was coming from the primary side of the bike but it turned out to be the cam chains, opposite side of the bike from where I was hearing the noise.