I used to have a 90 jeep Cherokee that had a similair noise issue. for me it turned out to be an exhaust leak by the engine that I could hear under it at idle. Plus a loose/warn out U Joint at the rear axle (it would rattle at acceleration and vibrate as well, but at higher speeds/rpms nothing. The u joint finally snapped a bolt on day, so after replacing it the loud rattle at acceleration that sounded like it was in my transmission was gone. It sounds like you might be tracking it down to your clutch, but it might be something to check out just to make sure all those bolts on the joint at tight.