Sounds like it could be one of a few different things.
First thing that comes to mind. Miss alignment of bellhousing to engine. If this is not indexed correct, the input shaft will be on a slight angle and be torquing on the input bearing. Making noise when clutch is not pushed.
Second- Makes me wonder if the flywheel is tight.
Third- Possible thrust bearing failure?
4th-Is the throw out bearing releasing from the pressure plate, not riding it?
