Yes, I've had the same symptoms and indeed the rotors were warped.
I also had something very similar but it was more to do with the speed
of the car, it would shake.. more... if I braked, and that turned out to
be tie rods (on my other car... A4).
ya, I put on some new pads, but didnt touch the rotors, because they cannot be machined. I guess with the new pads it just magnified the problem, I'm going to order some rotors off 1stvwparts and put them on, and try to save some dough
You do need a torque wrench as well to properly reassemble everything.
I'd gladly loan you mine, but there is the question of logistics.
I think mine (ft-lbs) was less than 70.00 at NAPA, and that was agood one.