This is a common setup prob, IMO from your decriptionI agree with K B, either your engine has moved and closed gear mesh, or more than likely, the clutch bearings are shot and seeing as you have to remove the bell, replace the clutch springs and shoes too as it may be them. You dont often get a clicking from the drivetrain itself, but it could be that a grub screw has com slightly loose on one of the front or rear diff input drive cups and its spinning and the click is when it passes it locating dent each time.