Did a lot of research on this subject for my Excursion. Went through 3 sets of rotors in 70k miles, all of them "warped" so bad the steering wheel would almost snap your wrists under hard braking.
Here's what I learned:
1) Very seldom do rotors actually warp. What most call warp is actually an uneven surface caused by "pad transfer" whereby the material from your pads bond to locations on your rotors, creating a high spot in relation to the rotor surface. The rotor itself almost never warps. There might be some truth to the rotor getting distorted by uneven torquing of lug nuts. Most OEMs recommend a 2 stage torquing; I do my first torque (using a star pattern) to 75 ft/lbs, then go around again to the recommended rate. Use a torque wrench, and don't let shops do anything other than HAND TORQUE your lugs. Torque sticks are notoriously inaccurate!!!
2) Ok, now that we're all technically correct, that doesn't make the pad transfer problem go away, does it? What do you do?
First, get your rotors turned, and new pads, if you've got a problem. If your rotors are past tolerance for turning, then replace. If the problem's not too bad yet, you might try scuffing your rotors with a scotchbrite pad on a die grinder--go easy though!
Second, ensure while you're doing the pad replacement, that your pins are in good shape and properly greased. (To the OP, don't worry about greasing your bleed valves--they were closed, so all you did was plug up the last bit with grease. Q tip should clean that right up).
Third, once you've completed your install, season your pads and rotors properly. High end brake parts will have directions for doing this, but it basically involves a series of medium braking events (5-10 times), with enough space inbetween them to allow the brakes to cool completely. Follow this up with another series of hard braking events, with adequate cooldown between times. Don't come to a complete stop during these events! (Obviously, a deserted country road at night is the best place to do this).
Finally, use your head when using your brakes! If you do a hard stop, don't hold the brakes in that position at a complete stop. You just super-heated the rotors and pads. Let your vehicle creep forward a couple of inches to put the pad in a new position. Better yet, slowly edge forward until the light turns green (without hitting the car in front of you), without completely stopping in any one position.
I've been doing this for quite a while now, on both my daily drivers and my mustang, and on SWMBO's Subaru, and it seems to make problems go away, and makes the brakes last a lot longer (particularly on the Excursion, which does a lot of towing, and is a big beast to stop anyway!).
