I was just reviewing some of my med school physiology after reading your question. When enough stress is applied to a bone to create microtrauma or microfractures, (such as what happens during the transition from shod to
unshod) the cells around the microfracture die and send signals for the osteoclasts (the bone cleanup cells) to come in and essentially clean out that area. This process takes about two weeks. Then, more signals are sent for osteoblasts (the bone manufacturing cells) to come in and lay down a matrix of new bone a process that takes approximately 3-4 months. Over the next three years, the matrix that was laid down continues to become mineralized and increases in density and strength to that of the surrounding mature bone. So, here's another testament to why we should not make the transition to minimalist/barefoot running too quickly.
This is at the same time overwhelming and pressure relieving. The soreness in my feet when I first switched to minimalist shoes could have been partially microfractures. I'm not just a weakling, there really is something that takes 4 months to heal in my feet, but it's possible every time I up my intensity too much at once that I will have this again, and it will be years before I reach full foot strength. At two months in, my microfractures should be starting to heal and grow stronger bone. The good news is that if I keep this up, and have good nutrition, I should grow stronger feet out of it.
I do feel like a patient recovering from an injury, but my injury was 15 years of bad body alignment. I can't be in a rush to get over it, but rather I need to be patient with myself, and push only a little bit on the edge to gently move myself towards better health.