Your chronic knee pain scenario sounds very similar to my experience with knee problems. Here's a quick sketch of what has worked for me.
About 3 years ago my orthopaedist said to ride a bicycle to strenthen the muscles around the knee and to run less frequently to give the knee some rest (my left knee). This worked somewhat for about a year, but the knee pain returned in a different location so I went back to the doc.
The orthopaedist explained that from my xrays he could see that I had a worn miniscus which would tend to send pain but not necessarily to the same location. He encouraged me to give up running. I was V E R R R Y discouraged.
I cut back on running and rode my bike more and more. I also started taking glucosamine/chondroitin which seems to help the knee produce more sinuvial fluid.
The bad news. I'm still running, but I limit myself to 10K's and 10 milers. I also stop and walk if the knee acts up (more than usual). I used to run through the pain which probably made matters worse about 3 years ago (before and during a marathon) which probably stimulated the saga.
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