I was working on this car at 3am with a friend. I don't know which one of us did this, but I have been kicking myself for days now. One of the pads was in backwards, so the steel side of the pad was on the rotor. I'm not exactly sure why the pedal doesn't travel as far, since the width of the pad is the same, but it fixed the problem. Thank god I didn't have the car towed in. Thank you all for your replies.