Do you have a neuroma? Also, exactly how wide are your feet? I have pretty wide feet and every now and then I'll see a pair of shoes that is "you know, sorta wide" and they might feel ok at first. Later on the pain begins. Since I bought the Sidi Mega Dominators (in a size 43! ) my feet have been so happy. Besides being truly made for wide feet, they have a nice ratcheting adjustment. Sometimes I like to wear my shoes tight, sometimes loose, and they are easy to adjust on-bike. Also, the Sidi's are extremely stiff compared to some other shoes I tried on, which means less flex and wear-and-tear on your feet.

Make sure your socks are big enough, and when you put them on make sure they aren't pulled around your forefoot too tightly. It might feel fine on short rides, but later comes the stabbing hot pokers. I'm fond of smartwool socks (especially the ultralight summer ones) because they don't compress my feet and I always make sure to wiggle my toes periodically.

Also pay attention to your stroke - do you tend to point your toes down? Even if your shoe and socks fit properly, you will be constantly shoving your foot into the narrower point of the toebox. I always struggled with pointing my toes down and recently a physical therapist told me that this is caused by having too-tight achilles tendon and calf muscles so he gave me some stretches that have been helping (my knees are also happier, as a result).

This is all assuming that you've had your cleat placement and seat/pedal alignment looked at by a pro.

One last thought - how were you managing your electrolyte levels? I once experienced some extremely bad hot foot/metatarsal problems on a monthlong walk that were caused by edema that was due to a mild sodium deficiency (hyponatremia).

HTH!