check the throwout bearing. You can see it by pulling off the inspection cover on the side of the bellhousing. Look in there and make sure its seated against the pressure plate correctly. When the clutch was done, was the throwout bearing changed? If not....why not?! It is VERY possible that when putting the tranny in, if an alignment tool wasn't used for the clutch, that you might have hit the pilot bearing the "wrong way" and fucked it up. Judging by the fact the noise goes away when you push the clutch in, I'd vote throwout bearing.