It has taken 2 evenings but I read this whole thread. Great work. While reading there were several people mentioning warped rotors. Have a look at the attached article. I have had "warped rotors" and fixed them with a power drill and wire brush on both surfaces just cleaning the friction material off. Its alot cheaper than the $400 rotors I was replacing at the time.
-Warped- Brake Disc and Other Myths