Ford Expy OEM rotors are known to warp and cause slight pulsing on soft braking and a vibration / shaking when hard braking (my 11, 14 and 17 all had this "undocumented feature" from early on (10K-15K) miles. I had the 2011 cut at 12,000 by Ford under warranty because it showed no pad wear. and it got new pads and rotors at 42,000mi. I had to cut the rotors at 60,000 because of the same issue reoccurring.
So, if you are experiencing this pulsing and shaking issue, the pads still have 50% or more life and the rotors have not been cut yet, I would get the rotors cut and it will resolve the issue. If you are having the issue and the pads are well worn, then replace both the pads and rotors. If you are not going to the dealer, then purchase premium pads and rotors and maybe they won't develop the shakes.