Tranny bad??

SxLxAxVxExN

Registered
So I took the bike out last saturday after the new motor rebuild and was riding it around all day and on my way home the transmission started clunking pretty bad. it is not a constant clunk but happens about every 3-5 seconds. It is deff. coming from the transmission and not the motor. I was not beating on the bike the whole day either and was shifting smoothly all day, but I did shift w/out the clutch quite a few times.
Any idea on what this could be? When the motor was out the tranny looked fine and we never touched it while putting the motor back together, so I'm not sure what it could be.
I'm just :please: that it's nothing serious and expensive cause I put too much money into this thing already.
Thanks
 
Does this clunking sound happen in all the gears? What happens when you squeeze and release the clutch slowly?
 
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