Yeah, you're probably right, Dr. G. Except, I got the shin and feet problems with the Vibrams. The PFT was the first time I ran in the Mizunos though. I think a combination of not having done a light run a couple days prior to the PFT to loosen the legs up, the caffeine, lack of sleep, and the crunches might have all contributed to a bad run. On a side note, I might have had some chest pain at about the 3/4 to 1 mile point, but I don't remember. If I did, it was probably from the caffeine. I remember distinctly wanting to quit because I wasn't feeling great, but the Marine Corps doesn't really care about how you feel, so I finished and eventually my only problem was the severe cramping.
I started doing some weighted toe raises by tying a plate around my feet, so I'm going to see how that works to minimize shin problems.