I'm no expert on this, but I had the same problem too, until I changed my rear tyre and put some dyna beads in it. The vibration has gone now, just after I was getting use to it. Would it be possible to have rear brake shudder if the rear wheel alignment isnt perfect. Some say it gets better overtime, so maybe the pads are just wearing parrallel to the brake rotor. Just asking!!!!! As someone said, I dont know why HD dont use a floating rear brake rotor.