I'm sorry you're in pain, have you talked to your doctor?
I'm not a medical professional or a personal trainer and everything I know about running I learned on the Internet but you could be hurting for any number of reasons. Are your sneakers new or worn out? Are you stretching after your runs? The stretching is just as important as the running. Do you do any strength training on the days you don't run? From what I've read weak hamstrings can be a cause of knee problems.
I'm in week 3 myself. I'm 49 and i haven't run since high school, but I figure if Menopause is going to wake me up at 4 o'clock everyday then I can put that time to good use. The first week my hips were bothering me because I was rushing through my stretches. Here's some that might help www.sparkpeople.com/resource/fitness_artic
| December Minutes: 266