Try these troubleshooting tips...
This is by no means an exhaustive list for the cause of pain when you're running. But it's a good starting place. Watch the video or read the list below and figure out which category you might fit into.
Read "Power, Speed, Endurance." Research the Pose Method for running. Hire a coach. If you're not going to do this then...
Don't step out too far ahead of yourself or lean back or slap your heels down hard and heavy. You should be stepping beneath or slightly behind your body (depending on pace), landing mid-foot / forefoot, and have a slight forward lean (again depending on pace), keep your head looking out to the horizon and minimize rotating too much throughthe hips / torso.