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An article that explains very well what is going on with knees and even hips regarding running (and walking). Search "Why The Heels On Modern Running Shoes Are Hurting Us" and you'll find the article (can't yet post links).
I have personal experience with one knee (for years) and one hip (on and off, but got worse several months before going toward barefoot). They've gotten much better after ditching knee and hip destroying shoes and correcting my gait, though not completely healed yet.
My advice is to run barefoot, as much as possible. And only use minimalistic shoes if you want to wear any. It takes time for feet to adjust and adapt, some months. At first, for a few months, especially lower calfs can be sore and tired and fatigued and painful (mine were), because having worn shoes all life the muscles are very atrophied. The muscles have to catch up with the rest of the body, this takes time.
Another thing is adjusting and adapting soles. I specifically exercised walking on a rather rough surface. At fist it was painful, only managed a few steps, but as the sole muscles adapted and adjusted I could walk farther and farther, now it's massage-like walking on such surface.
A forum where are people who've been at it for years. Though I'm not a member there myself. Search "thebarefootrunners" and you'll find the forum.
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