Some Thoughts on Pain for New Barefoot Runners
1) Switching to running barefoot causes a lot more changes that just on the surface of the sole of the foot. There are lots of interconnected bones, tendons, and ligaments throughout the foot. When you switch to BF, these are suddenly called into play after being mostly dormant and atrophied from being in restrictive shoes for years. Like Ken says, try wearing a cast on your arm for 12 months and then see how strong your arm is when you take it out.
So your pains could be the inside structures of your foot adjusting to the new uses demanded of them. At first, your foot is likely to respond with some cramping and pain - trying to resist the changes. This is why you want to start BF running slowly and build up gradually - let those bones strengthen and those tendons stretch.
2) Also, shoes have a tendency to deform the shape and structure of the foot components. These need to readjust and move to new positions, sometimes, which can be painful. (Ever wear braces on your teeth?) My feet have gotten wider and flatter (laterally) and my arches have increased (axially). Yes, bones can move and tendons can adjust their length, but they complain in the process. If you push the changes too hard or too fast, you can end up with stress fractures, so be careful and don't over-do it!
3) There is correct BF form and incorrect BF form. Bad form causes more pain and problems than correct form does. After running with a certain form in shoes for years, your form does not magically change just because you kick off the shoes. The pain in your feet might be the result of some lingering elements of bad form. Study the basics of proper BF form and practice them. Sometimes its harder to re-train the brain than it is to re-train the feet and legs! My own challenge has been to remember to place my feet *beneath* my center -- not out in front, and to keep my knees *bent*.
Early on, I noticed that I kept drifting back to my poor form ways. To overcome that, I had to toss out any idea of running fast or far at first. I would start a run by literally just running in place, freezing in my brain that feeling of BOF placement beneath my body, bent knees, etc. -- then gradually leaning into it to get forward movement. As long as I could keep that same feeling as running in place, I kept on going. But as soon as I noticed I was putting my feet too far out in front, I would stop, and begin the process all over - running in place, etc. This way I was not practicing running with bad form; I was forcing myself to run with better form by interrupting the bad stuff.
Lately, I remember to place my feet beneath my body by telling myself that I need to step within my shadow at high noon. It might not be high noon and I might not have a shadow, but I know where it would be and where I should place my feet. Even when running faster, and my legs are lifting backwards higher and my knees are driving forward with more intensity, I still place my feet beneath my body. That is the 'happy zone.'
Still running and loving it!! -- Ryan