During or after Iron Will's x-country ride earlier this year he mentioned purchasing a good pair of padded shoe inserts that made all the difference. I think he said something like "I bought the most expensive pair I could find."
I removed the inserts that came with my Sidis to make room for my orthotics which I wear to support my high arches. The orthotics stop just in front of my arch, so there is nothing between the ball and toes of my feet and the shoes.
I don't do a great deal of walking during rides and the ball of my foot (rather than the arch) is on the pedal, so I wonder if I really need to wear my orthotics in my bike shoes.
I've seen some inserts in the LBSs, I believe they are Specialized or Sole, that conform to the shape of one's foot using heat and are made for different arch types.
BTW, I do not have ANY discomfort in these shoes (the SIDIs) even at the mileage point where my right foot was screaming in my other shoes. But on much longer rides there may be heat issues and I'd like some padding between my foot and the shoe.