Throwout Bearing?
What stops turning when you depress the clutch? The tranny input shaft. Sounds more like a bearing on the input shaft or something internal in the tranny to me if it stops when you push the clutch in. The TO stops when you release the clutch and it retracts away from the pressure plate. It could be the pilot bearing in the end of the crank as well, but that normally keeps the input shaft turning making shifts difficult because the input shaft isn't stopping or slowing enough for the synchros and balks to line up the gears for shifting. If it were the pilot bearing, the knock generally goes away when the clutch is engaged (pedal released) because the input shaft turns at the same speed as the engine. But, if you have a bad release finger in the pressure plate, it could be hitting the TO. That's normally accompanied by some pretty bad chatter on start off, and some serious vibration. Push down very lightly on the pedal until it just starts to engage the pressure plate with the TO, and see if you feel any pulsing in the clutch hydraulics. It will be very light and hard to notice, because there is an orifice in the line between the master and slave to help reduce chatter.
Are you testing with the tranny in neutral, or in gear (rolling)? See if you hear the same knocking noise when you start moving slowly in 1st, versus when you release the clutch in neutral. Having it in gear may put some loading on the input shaft to keep it from knocking, but I dunno. I've got some mild noise that I feel on the stick more than I can hear, and I'm sure I've got some stuff going south in mine. Last two fluid changes, I had a couple very ominous looking chunks of metal on the mag plug, and the metal 'dust' accumulations are certainly getting worse. I just hope it holds until I can find a good M5 to rebuild and hang in there. I need to be able to swap it in without having the truck down for weeks for a rebuild. No way am I going to let a dealer near it again.






