Your pics are low resolution, so can't really tell what's going on, but that middle pic looks like the rotor has heat-spotted. You can almost see the "ribs" showing through the rotor wearing surface. That happens because when the rotor get really hot, the areas that are tied to the vent ribs underneath get hotter. This is because those areas do not benefit from the axial cooling air flow cannot cool as well as the areas between the vent ribs. Once your rotors have heat-spotted to a severe enough degree, their structural integrity is compromised and you'll start experiencing problems, including vibration.
Not clear on the exact history of how you run your brakes and when you did what, so cannot tell what exactly happened. It is possible that uneven brake pad material deposits caused the hot-spotting. Again, it's impossible for any of us to tell from a few grainy pics. A lot can happen in 6000 miles.