When I did a bike fit, they started with the cleats and feet. Almost everyone can do with shims under the cleats and replacing the standard soles that come with the shoes.
The shims make the surface of your shoes level with the natural angle of the bottom of your feet.
The soles provide support for the arch of the foot. Standard shoes provide very little support as they also need to fit people with very small arches.
I was not feeling pain, but before the adjustments both my knees were moving a bit left to right. After these adjustments this was solved. What I noticed is that my feet are now much more stable as I apply force during the pedal stroke, even though this was not something that was bothering me before.