My knee pain early on was due to my cleats not being situated properly on my pedals and me mashing through, instead of spinning.

I then bought SpeedPlays (with float) for my clipless pedal...and I learned how to spin.

After about 2 months, my knee pain was all gone. And I had acute knee pain. It would hurt so bad, I would have to pedal with 1 leg at the end of a ride.

That's what worked for me. I'm not a Dr. or a professional, so I can't say what will work for you.