Running is high-impact cardio, so it's a possibility your knees and back can start hurting. You are starting to get in shape right? Have you done any strength training (eg. lifting weight?) It could be from being top heavy, without doing much for your back.

Do some lower-back exercises. It's the most overlooked part of the body to exercise, but I think it's one of the most important. It's great for your posture.