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Do this too: pull off your rotors and get a wire brush and some brake cleaner and scrub as much dirt and rust off your hub, back and front mating rotor faces, and wheel mounting face as possible. Once you've done this, put a very thin layer of antiseize on those same surfaces.
Rust chunks can cause precisely what you are describing by forcing the rotor out of parallel with respect to the calipers, which would be felt as vibration even with brand new rotors and pads.
I have a feeling based on the symptoms you described that this is what happened to you. I always clean the mounting surfaces when I do my brakes for this very reason, even if they don't look bad.
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