Just thought I'd update people reading this thread. I'm currently under physical therapy for my shin splints, and I believe I can be in full action (and I mean full) in maybe 1 month. While my feet could have been a problem starting out, I pretty much strengthened everything down from the calf. My problem wasn't at the feet (or it could have been, but i fixed it), but my overly tight calves, hamstrings, and hips, as well as a weak tensor fascia (not sure about the name, but its the muscle on the outside of the hamstrings).
I did stretch my calves since I had this problem, but my incorrect form meant that I didn't really stretch them useful.
In either case barefoot/vibrams running and walking around is great, and probably helped a bunch, but just saying anyone suffering from what I had that there could be possibilities of biomechanical problems that are hard to diagnose by yourself.