If it's the left side of your right knee, try moving your right cleat for less toe-in on your right shoe. Maybe shift it back toward the heel a few mm while you're at it.

I had a mirror image of your prob -- right side of my left knee -- and that worked for me.

Also note, if you moved your seat fwd, you might want to raise it a couple mm to compensate for the shortened distance between your hips and the pedals.

The problem for me wasn't at the bottom of the stroke, it was at the top -- left knee flaring outward and too much toe-in on left foot.