I am nowhere near expert on foot injuries, but if your are a bad over pronator and flat footed, IDK if barefoot will really fix that. It could, and some smart person may know why, but from what I have learned, if you are flat footed and an over pronator you might need a shoe with a decent medial post for arch support, and straitening out your achilles. The orthotics could help too. There are some good books out there, I read "Fixing Your Feet" by John Vonhof when I started doing a lot of mileage last fall. It is a gold mine of information and lessons learned from a plethera of distance athletes. Here is what is says (some of it) on PF:
"generally prescribed treatments include rest, moist heat and streatching in the morning or before activity, icing massage after activity, heel cups, taping of the foot for arch brace, orthotics, foot exercises, and shoe modifications."
"motion-control shoes can help if you overpronate."
"Most men stop when they begin to tire. Good men go until they think they will collapse. But the VERY BEST men know that the mind tires before the body and push themselves beyond all limits. Only when all of these limits have been shattered can the unattainable be reached." ~Dan Gable