Search through posts and threads over the last week or so which have dealt with "leaning out lower body" etc because I detailed in those the kinds of lower body workouts I now do that prevent and treat patellofemoral syndrome, i.e., runner's knee.
You need to change the way you work the lower body so you can continue to run without pain. It is possible. You may need physical therapy to help teach you specific exercises you need as a runner to stay injury free.
Also, go to runnersworld.com and start reading up on patellofemoral syndrome, the most common of the runner's knee ailments. This website also has video archives of excellent exercises, including core training and balance exercises and one legged exercises, which can treat the problem and prevent it recurring.
Clare