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I have an '06 HD Dyna Wide Glide. I find the ride to be smooth at all speeds. However when ridding 2-up my wife complains of teeth chattering vibration. I'm just not feeling it. The pegs are tight, the sissy is properly connected. Does anyone have any ideas/suggestions on what to check next?

Fender struts, and shock mounting hardware. If you don't have the torque values, you might want to be sure you have it right, especially for the shocks.
Oh, and where the rear fender connects to the frame. Any of that would vibrate right through the pillion seat.