So as a follow up to this problem, now that it's fixed...
I replaced the front right hub thinking the slightly bent/off hub was causing a problem, and it didn't fix it. I reluctantly took the car to Watkins Glen on Tuesday for a HPDE and worked up to speed, making sure the brakes weren't going to be a problem. The shudder really wasn't that bad and seemed to actually almost disappear by the end of the day. Needless to say stopping from 120-140 to 60 over and over again has fixed my problem. lol It must have been a pretty good uneven layer of pad deposits. What threw me off though is that I did try re-bedding the pads and used the correct procedure and it didn't help one bit.
In conclusion, track day fixes cars.
lol