The pain is not necessarily from the bike or your pedals. I'm also a Speedplay user and I started experiencing knee pain. Because I had been diagnosed with chondromalicia and everytime I see an ortho the cause is attributed to the chondromalicia I put up with it and faithfully kept my quads strong. By the end of the summer my pain had progressed into the back, piriformis, and foot. The ortho treated each area as separate issues. I tried shims in my shoes and had professional orthotics.

My bike fitter recommended seeing a PT who did bike fits so I did. It turns out I had a locked SI joint. Apparently it had been like that for years and caused my right side to weaken.

Now that I know the real cause I work on keeping my glutes strong rather than the muscles around my knee.

I've also quit using orthotics for skiing and walking. Haven't ridden yet this season so we'll see what happens without them.

BTW, one of my symptoms is I always sat a little sideways on my bike.