Thank you all for the feedback and ideas. I didn't get a chance to tear into it again this last weekend but hoping to get into it again this weekend. The rust build up on the hub is what I'm hoping the problem is as I didn't do any kind of cleanup after removing the old rotors (First time replacing rotors). The car drives fine otherwise (No howling or severe road noise) and doesn't wander or pull to either side. I had a new set of Nitto Motivos put on it in Feb of 2014 and have put less than 3000 miles on them. When they did the outer tie rod ends in December they also did a tire rotation, balance and alignment (Braking issue existed before the work and after). My next idea was to replace the front wheel bearing hub assemblies and although they aren't super expensive they aren't cheap either.

 

If you do replace the hub assemblies, get the good ones, MOOG or Timken. Don't waste your time on the cheap ones. And put anti-seize on the mounting bolts as well as the face where the rotor makes contact.

Fun Fact: It's technically impossible to "warp" a rotor. Rotors are cast in temperatures (2000F) much higher than your brakes will ever produce (normally 4-500F). Uneven rotor wear, which is incorrectly called "warpage" can be caused by something as simple as incorrectly tightening the lug nuts or as major as a the slides sticking causing the pad to remain intermediately in contact with the rotor in off braking situations. That creates uneven wear on the rotor, creating a pulsation in the pedal.

 

Took my car into another shop yesterday and got it back today. The brake issue was diagnosed by them as.... 4 warped rotors! I had them turn all 4 of the old rotors and had them give me the new Autozone ones back which I plan to return. Braking issue has been resolved so far. They also replaced a worn Transmission mount which they said was bad (Gear shift raising when accelerating) and so far the car shifts smoother. Hope the issue stays resolved for a long time!