When I use to run, I had knee issues too until I changed the shoes i wore and started stretching properly. I specifically went to a running shoe store and got a different pair of shoes. Then I started doing a stretch they recommended where you sit down on something, put your foot over top of your thigh and push down on your knee as far as u can. It looks like u making a chicken wing with ur legs. It sounded ridiculous to me at first but after I started doing that, my pains just went away completely.
