Have you ever had anyone with some expertise like a LBS check you and the bike for fit? Or had them watch you ride? Any chance you could have someone video you riding, so you can watch yourself or show a fitter or Dr? I'd talk with my doctor too.

I have knee pain from riding but it is related to both rheumatoid and osteo arthritis and bike riding helps lessen the pain. It only hurts when my knee is contracted and not when it's extended. The first few minutes of a ride are painful but it gets better as I go and when I am in full riding season it's only a matter of a few cranks to have the pain go away.

When I'm feeling exceptionally stiff I only pedal with one leg for the first few cranks and that's no easy feat considering I am not clipped to a pedal. The pain I experience is almost all on the front inside of my kneecap, but I know that I have no cushioning left in the joint and it's bone on bone.