I just ran across a thread of yours with video of a knock. If that is the reason for pulling the tranny, I am guessing you have an external slave cylinder for your clutch. If so you will see a shiny spot on the throwout bearing fork where it is contacting the pressure plate causing the noise. If I am right, replace the clutch disc (which will be totally worn out) and check the fork for a crack or a bend, replace the fork and your noise will be gone. (I hope I am right on this one)
Edit: If you have an internal slave please disregard this post!