Confounded variables. Too many. But, you are on the right track. Isolate them. Control them. There are professionals who can measure your leg lengths and find a difference, but something is up. Is it the saddle? Loose bolts? Pedaling? The skeleton? Muscle strength? Pain is your guide, unfortunately. The pedal connection issue is another factor, for hips as well as knees as well as...it's a system. Seek balance. Check your mileage changes, effort changes , general health (age?), too. Molestem senectutem. Unless it's painful because of the saddle, it could easily be from another cause; changes in shape are "breaking in", are the virtue of leather. No one is symmetrical, but overuse is a cause of pain, and position can trigger overuse, as can being restricted in movement. Wiggle and stand lots.
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