sounds like something similar to what happened to me....it would start to clunk in 3rd on mine, becuase i had bought a new chain and didnt know it would be best to replace the rear sprocket. I looked at mine and it was basically worn down to were its not usable anymore, and i also thought it was the tranny.
If you recently replaced you chain, try a replacing your rear sprocket.
hope this helps. :baseball_original: