Here's a client who gets knee and lower back pain when running. I've been working with him for a couple of months now and I think he's an interesting case study.
The video is from the first time I met him. Unfortunately I did not take a video of his running before I had given him some technical cues. Prior to these cues, he was running with more of a forward lean and landing excessively on his heels.
The client was stuck in a bit of a vicious circle. He had weak knees and under conditioned calves. This meant that his knees and back hurt when he ran (conditioned calves effectively absorb the impact of landing). To try to manage the pain, he was running in a slightly peculiar way. However, by doing this, he was not strengthening his calves and quads.
The solution? Break the vicious circle. Strength exercises to get the quads firing up (they were very reluctant to work!) and those calves stronger. Then running lower volumes with good technique.
The result? Without any really hard running, he's knocked 90 seconds off his 2.4km time, the pain in his back has disappeared and his knee pain has improved considerably.