I had a similar problem that took me several years to solve. I had a consistent pain on the outside of my left foot and, to some extent, on the outside of my right foot. I tried different shoes finally settling on the Sidi's in their Megas (wide). But that still didn't solve it. Wedges under the cleat helped. Finally I did a pedal fit with a good speedplay dealer with their fit kit that has different length spindles. Turns out I need a wider q factor that is solvable with longer spindle pedals from speedplay. Completely solved the problem - no issues. Wedges came out from the cleats and I'm good to go.

Speedplay has a new mtb pedal out that has float like their zero road pedals. They tell me that they are going to offer different spindle length pedals there too.

Work on this by first getting good insoles - I like the Specialized ones that you can get to match your arch height. You can't really go after the other issues until your foot is stable in the shoe.

J.