Just guessing here, I think you may still have a warped rotor, rim not seated on the rotor. You could try putting the suspect tire/rim on the back and see if it changes anything.

Another source for bad wheel shake during braking I have seen on some other makes is worn/ sloppy control arm bushings... but, like David said, they usually aren't as noticeable without a warped rotor to accentuate them. 

Even if they are new, doesn't mean they aren't warped.  Especially the lesser expensive Made in China stuff that the majority of the parts stores carry these days.  I put some new ones on my Subaru a while back that have just a slight little shudder to them.  But, since they cost me about $24 each vs about $90+ each, I think I can deal with that. 

Travis. It seems unlikely since the SW. Came from Boston and the roads a so good up there. And the car is only 17 hrs old...... Kidding.   It runs straight I,ll take a better look.  Sc

After the timing belt looked at this  shimmy brakey .
Took the pass side breka off and disc off.  made shre the rust and surfaces were clean,  reinstalled .  did not help.   Jacked up the front end an shook wheels around
 it seems the driver side outer  tie rod is the shakeyest.

I had rotors turned and they still shaked.  I got 2 new rotors and that fixed it.  Maybe thin rotors are bad.  I don't know but I'm happy its fixed.  SC