I have a 2014 electra glide, it had pretty bad brake chatter so I assumed it needed rotors replaced due to warpage. Bike has 11,000 miles. At this time I replaced my lower legs and chromed out the front end, replaced the wheels, with new bearings, new tires, new rotors and new brake pads. After all that I take it for a ride and have the very same brake chatter. Primarily front and at the first hit of the brakes it does it, any speed, It chatters hard enough the front fender rattles. Could it be faulty abs pulsating at any touch of the brakes? It is almost unridable.
Agitation in

 

Could be an anti lock brake problem. Maybe a defective wheel speed sensor?, Assuming you installed the anti lock wheel bearing correctly. Also I would rule out the ( new ) rotors with a dial indicator.

 

I had it on my old Dyna too. I pulled the pads off and filed the leading edge down so that the pad isn't at a 90 degree angle with the rotor. Stopped the chattering and squeaking instantly.

 

A little chamfer on the leading edge helps remove any vibrations that may come up from use. Good job. And something I do as well.