Becca, what did you do to your foot? I did a couple of things to mine including a stress fracture and a posterior tib strain with some tendonitis to make it all complete.

I use clipless (sometimes) on the road when I'm commuting. I think you have the same shoes that I have and they are..well..not very good for my foot. I need a wider toe box. Until I find the right shoe I won't be riding clipless because physical therapy really is painful.