[patrickt]

If the alternator checked out, and the VR is not broken, check the continuity of the field and stator wires running between the VR and the alternator, and check the continuity of the the orange wire running from the alternator to the fuseblock. Then double check the grounds to both the alternator and the VR and, if all of that checks out, and the connections are tight, then it is metaphysically impossible for the system not to charge.