Just ran 3 miles with no pain after the first half mile or so (practically my warm up). My route is pretty hilly at the beginning and flat for the last mile, I got going pretty well. The pain is in my right knee which is my power leg when I start, so it's quite likely I did something toward the end of the track set (100m) I did a week ago.
I'll definitely add some of the exercises you guy have mentioned into my regular routine. Thanks for the help.