not sure what happend

ok i have a 91 ford mustang all stock i just put a new clutch in and everything and after driving about 3 thousand miles something weird happens and im not sure what happend there is a noise what sounds like its coming from the bell housing but it is raising alot of noise and i think that it is the throwout bearing but not sure it still runs the same but there is this loud ass noise that kind of sounds like a rollercoster going on the tracks but i am just wondering what it could be

when ever i push in the clutch the sound would stop and whenever i am parked and put it in first the sound will stop all of a sudden but when i put it in neutral it will start making the noise and the noise is like a clunking noise and when i drove it home when i went to 3rd gear it was not as bad but was still doing it and all the noise is coming right from the bell housing and at the back of the tranny i found that one of the bolts was backd out a little not sure why because we tightend them down pretty good so i just tightend it back