I know this thread has been idle awhile, but I thought I'd give an update for anyone who might come along later or whatever.

It was totally the rear rotors.

I finally switched them out last night and everything is smooth as normal. Yay!

I'd heard this somewhere before, and I'll subscribe to it from experience:
Braking Vibration:
If you feel it in the steering wheel, it's the front rotors.
If you feel it in the pedal and/or in the body of the vehicle, it's the rear rotors.

I also went ahead and bedded them following what I remembered from this article. I basically just sped up to 60 - 70mph and hit 'em hard till I got down to around 10pmh, and did that 10 times or so.

I wasn't sure last night, but the brakes seem a little soft today. I'm sure it'll be an easy fix - adjusting the pedal or whatever. Or it might just be that I'm not used to the thing slowing down smoothly without vibration.

 

The guy at Les Schwab said almost what I have found, but may not be your problem. If the hub is not clean or square, then the rotors will wear unevenly. Eventually the two surfaces of the rotor will not be parallel (actually coplanar) and the pulsation of the brake pistons going in and out can be felt in the brake pedal. I had this on a different car, and cleaned rust off of the hubs and it took care of it. Apparently, the auto manufacturer's are machining the rotors after mounting them on the hubs when they assemble the car, so the hubs don't have to be square. But then when the rotors are replaced, they develop this problem. But the problem only develops after a while, so it seems that your rear rotors must have the same problem too, since it only gets a little better when you replace the fronts. It could also be that your brake pads are not moving on the rails, so you should make sure that you put the stainless steel guides in, and lubricated them.