Matt, I have had similar problems. I ended up finding out that I have a stock spring (front left) that has cracked and broken on the bottom ring that makes contact with my a-arm(turns out thats common with the Focus and our cars...). Now I am not saying that this is your case, I know that you have some suspension mods sooo if I were you I would go through those mods before doing anything with your brakes.
My advice may seem way off from what you are thinking but I say give your suspension a real good look over. Does this vibration feel like its one sided? Is it more front orientated or rear? I always had a bad feeling about my Brembos, thinking I had done something wrong either with the installation or the break in process (which is sooooooo much fun!)
I put my rotors/pads through some heat cycles (as stated on the Baer website) and I know for a fact that I did everything right. So I am saying check your suspension mods out before doing anything to your brakes.
Also, have you gone through any puddles while your rotors were really hot? This may have warped them so until you can rule your possible suspension delima out you shouldnt start thinking that they are alright, they could be warped which sucks balls cause they cost an arm and a leg.
Oh yeah one more kick in the balls (did I say that already?) You cant turn slotted rotors and I am pretty sure that you cant do that on drilled rotors either. I wanted to get my 13in slotted rotors turned to fix my vibrations but its not possible so you have to get new ones.
Good luck with everything and I hope my advice/suggestions help.
-fawcett
