I injured my knees two ways in high school both by hyper extension.. Once by slipping a pedal on my BMX bike and somehow smashing my knee on the stem and hyper extending it as well. Second time was @ Wrestling practice and the guy I was wrestling with (from standing position) "ankle picked" me and drove his shoulder into my knee - hyperextending it again. I never went to the doctor, just wore a brace until the pain went away and kept riding and wrestling
Year later, found a similar pain when doing heavy squats and that was mostly due to poor form.
The pain came back when I had kids and I was 40 pounds heavier and out of shape... It was caused by crawling around on the floor alot with the kids.
Again, never did anything about it just tolerated the pain and it eventually went away.
Now - in the past couple years, I've made significant efforts to lose weight and get in shape and running played a key role in that. My knees started hurting in the early stages but I then researched and invested in a good correct pair of sneakers + working legs in the gym with good form seemed to rehab it. Now I can run forever with no pain. However, I do know when I need a new pair of sneakers because pain starts to sneak in with my feet, ankles, knees and hips. I buy a new pair and I'm back in shape again with no pain.
All that said, I don;t think I added much value here - have you tried researching and investing in a correct solid quality running shoe and have you ever tried to research and do knee rehab exercises and stretching before / after running?