Shoes aside, let's talk foot pain
I have been riding for a decade or so now...on and off. I have a Road bike and a Mountain bike, I have road shoes/pedals and SPD's. After riding my second El Tour de Tucson, which includes a couple of wash/ "river" crossings (I say "river" because they are rarely running so it's a hike through 4-6" of sand) I decided to put SPD peddles on my Road bike. I've never gone back. I have the Sidi Dominators, my only complaint; they're black and in the Tucson summers black is not a shade of choice.
I too had problems with pain in the balls of my feet. It all comes down to how much pressure you apply to the ball of your foot while riding. I have learned to ride as lightly as possible. This means using the connection of the shoe to the peddle to my advantage. When you pull up and scrape back for peddle strokes, you do no need to apply much pressure with your foot. In fact, the only time you need to apply the full pressure of your foot is out of the saddle, you have no choice.
I also make sure my foot has some wiggle room. I wear a size 6 street shoe, which translates to a 38 cm. I wear a 39 cm in Sidis. This way I came accomidate expansion of my foot during long rides and summer heat; not to mention thicker socks in the winter.
Hopefully by now, you have already been taught this by a good coach. I am fortunate enough to be married to a world class bicycle mechanic and coach.
Supercutie