Overtightening the clutch bolts will not hurt untill one breaks. Some bolters claim they have been running them for a long time without a rear mount with no problems. I put an aftermarket crossmember with a mount mine. That long aluminum tranny is not made to hang like that. I can,t imagine what that noise is. I,ve heard the floor on the AD,s are pretty close to the trans. If it is contacting it it would make noise. Did you check the pilot bushing?
