You could consider getting stiffer mountain bike shoes, such as the Sidi Dominators (which have a strong following among TE ladies, myself included, I must say). Just as stiff as road shoes, but "walkable" (to some extent) and compatible with your current pedal system.
I did have ball-of-the-foot pain with my "softer" mountain shoes which were in fact touring shoes. The soles were really flexible, good for walking even a fair distance (not miles and miles but still), but very painful to cycle more than an hour in. But not all mountain bike shoes are soft.
Edited to add: As far as shoes are concerned, what you pay is often what you get. I find the top-of-the-line shoes too expensive for what they offer, but in the $150-250 range there are very reasonable options. Cheaper shoes have not worked well for me.