4Willia4 from what you are saying here it sounds as though the clutch assy. isn't aligned properly to the flywheel. Remember we are talking about a rotating assembly like a tire would be. Don't you balance a tire to take out vibration because one side is heavier than the other side? Same principle applies here also. If the clutch and pressure plate isn't aligned with flywheel then one side or the other becomes heavier and sets up a vibration that will be heard through the TO bearing. Since you have it apart get yourself a clutch alignment tool or another input shaft same as your tranny. Hopefully this will cure your noise. Also IMO I"d recheck that TO bearing ID size as compared to OD of input shaft. Just to be on the safe side. Just my .02$ here.
