Well, it looks like the dearlership finally figured it out. I've put 2,000+ trouble free miles on the Jeep since I last got it back from the shop. YAY!
I'd felt off and on vibrations still, but it was the burning brakes smell that really alarmed me the one night, and I took the Jeep back to the shop the next day. Turns out the brake pads were already almost down to the squealers (again).
After my 2nd new set of brake pads and rotors (not including the set it came with), I got new calipers as well. Still not fixed. But finally... the brake booster. They had it for just over 3 weeks (this dealership supplied me with an old Stratus as a loaner), but apparently they found the culprit. I didn't want to get excited right away, but 2,000+ miles with not one vibration has me believing it's finally fixed.
OK, time to order those skid plates and tow hooks that I wanted to get last year! Oh, and to call the guy up at DC again and see if I can get a deal on an extended warranty, cause who knows what else the thousands of miles of vibrations will end up having damaged down the line...