Jay Dicharry has a video out on foot self-evaluation for barefoot-style runners.
I don't think you need to do this prior to starting barefoot-style running, but if you have any problems with the exercises he outlines, you're more likely to run into trouble.
These are issues I've battled with, and Lee Saxby passed along Jay's advice. It was a big help, and resolved some issues immediately. See the label "Saxby" for more.
(Here's Pete Larson's take, this was the link behind Jay's name originally, I decided I should be linking directly to Jay.)