I did run in shoes. For awhile I actually did all my long runs in normal running shoes, my medium length ones in my frees and my short ones in just my bare feet. Just be super careful, because you are going to weaken your feet a bit while they are getting stronger and you are more likely to fracture them even when you are in shoes. My suggestion is run in shoes like you would if you were barefoot. So no sprinting, no racing down hills pounding away ect.... When I hurt myself that was what was to blame.