normally, no clunks are heard. you might hear a clunking noise if you let off the clutch fast....thats the release fork swinging back towards the trans. if you have an 03 with 17k.....you need to be changing all of your fluids. its recommended at every 30k, but you're due.....overdue by time. i have seen that the pivot ball for the release fork breaks, normally it makes the pedal harder, but i can see that it makes a clunking noise cuz the fork isnt staying in the correct position. def sounds like something with the clutch area, nothing trans internal or external. time to remove the trans