It is very unlikely that the swingarm bushing or motor mount is bad on your 2012. HD motor mounts are made out of much better material now than the earlier motor mounts were. The swingarm bushing is pretty stout and the only time I have heard of the bushing going bad is on the bikes that pull trailers.
I would think the rear rotor may have a little warpage in it to cause a vibration or pulse.
The front rotors are notorious for warping, the rear rotor is thicker than the front rotor is so it is less likely to warp but it can happen.
Making sure the alignment is good is important but I would find it hard to believe that it will cause vibration or pulsing in the brake system.
Also a check of the wheel bearings should be done, the rear has 3 wheel bearing with 1 of the bearings in the rear drive pulley so don't overlook the pulley bearing. My rear pulley bearing went out around 40,000 miles.
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08 FLTR candy red sunglo,with 2015 103 HO, V&H Dresser Duals with Monster Rounds, Power Vision tuner, Willy Shiny Wheels and Forks and a bunch of other stuff.