New knee pain

[OakLeaf]

Just visualizing it, it seems to me that it would make your seat height effectively too low, not too high. A taller shoe would decrease the distance from saddle to pedaling surface.

Knee pain (and swelling) similar to what you describe is what happens to me when my knees are bent too much at the top of the pedal stroke - though I never had an issue with sole height that I'm aware of. Right in the lateral notch between the patella and femur.

Maybe just try raising the seat height a millimeter or two.