As you knnow, the knee pain could be from anything. Just a suggestion of what it could be from experience, if you run on the same side of the road all the time it's possible that some added strain is imposed on the leg which is higher up on the slope (most roads are sloped outwards for drainage purposes). Even though this slope is tiny it still can have an effect, running on the other side of the road when you start feeling the soreness MIGHT help.
Anyway, have fun swimming in circles with your giant right foot

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