I started using those cool looking Vibram shows a back in March and had some good runs. Until it started to hurt... and now I know why.
I've always known my foot was a little different than most others', as my 'Big Toe' isn't all that big. I always thought it was just the toe itself. WRONG
X-Ray of my foot
After having a summer of not being able to walk barefoot, and not be able to run more than around 2 miles before the pain forced me to stop, I went to a podiatrist. As it turns out, the phalanges behind my right 'big' toe is what's short. As a result, rather than having the pressure from my foot strikes distributed evenly across my foot, it's mostly focused on the center two toes. And that's what's causing the pain.