Well, adjustment is part of replacement. So you have to be sure of your adjustment.
This is to make sure that the throw-out bearing is nowhere near touching the clutch fingers when the engine is running.
Since changing the throwout bearing didn’t change the noise however, it makes adjusting even more important so that you know that it is not the thud bearing touching the clutch cover/pressure plate.
If it’s adjusted properly, and the bearing is not touching the clutch, then the noise you’re hearing is unlikely to be the bearing.
If you release the clutch rod completely, and allow the clutch fork to retract fully, and the noise goes away, then you know it needs adjustment.
If the noise does not go away, then you need to track down something else.
It’s very possible it could be the front input bearing of the transmission at that point.
When the clutch pedal is released, the transmission is spinning right along with the engine. When you push the clutch pedal in, it releases, and the transmission will stop spinning.
If it’s in gear, it’ll stop spinning immediately. If it’s in neutral, it might take a second or two to spin down.
Does the rattle go away the instant you lay your foot on the pedal or do you have to push and disengage the clutch fully before the noise goes away?
That could be another clue.
It would be very unusual for it to be the clutch itself, but I can’t imagine that it’s impossible.
Be a shame if it is, but you should be able to find out with all this testing.
And make sure the noise isn’t coming from somewhere else being transmitted through.
Even though this is a really long shot, remove the belt(s) from the accessories on the engine and see if anything changes.
Doesn’t take too long, so it wouldn’t hurt to know. Way out in left field, but stranger things have happened!
Good luck
