Anyway, after one such stretch of barefoot, I felt what I thought was a pebble or knot under the joint where my pinky toe connects to the middle foot (meta-tarsal?). It wasn't too bad, just kind of weird. I put my shoes back on after running about 5:00 barefoot and did the rest of my long run that day (this was my routine. add some barefoot into the middle of another run during the week. not always the long run). Anyway, nothing bad that day, but I took a couple of days off, and then went out for a couple of runs the next week. Went out for my long run the next weekend and 5 miles into my run, the pain got worse and worse and I had to walk (limp) home. This was back at the end of September.
I tried running a little here and there, never too long, but eventually started feeling better in December, but I didn't want to push it, and the weather was crap anyway. Anyway, I've brought my weekly mileage up to the high teens and am going to keep it there for a little while. In the meantime, I thought I might try to put some barefoot back into it but I'm trying to find the confidence for it.
I think that my injury could have also come from not taking enough time to recover from the half-marathon race. It was a tough race and I never really took much time to recover for it. Secondly, I've started to notice that my left foot tends to flop a little bit more than my right. Over the last year, my two injuries from running have been on the left side. Once it was a knee - not a stress fracture but something, and the other was the foot.
2014 Goal -- Run 5X per week, pain-free (relatively) by end of summer.
Creator of RunForth | @robraux | shodless.com
your left side only issues...do you only run at traffic? That could lead one to think you may be having issues from the curvature in the road, make sure you switch up sides of the road so each leg gets the experience of dealing with having to reach a bit further than the other and deal with the dropoffs and such that a should of the road brings.
The pain you got is a little weird to call. Going shod to unshod is a shocking transition to the foot, so just be sure your slowing WAY down when unshod and ensuring your feet stay under you and your form is good (I try to keep the pose method posture in mind).
heffa47 could also be onto something with the stone bruising aspect of barefooting. You very well may have hit a stone or any other number of objects that caused you deep bruising. Those deep bruises get hard to distinguish from "oh its a bruise" to "oh, I could have an actual injury"
Just listen to your body and go really really really slow with a focus on form and technique, not speed or distance or any other variable.
Barefoot and happy
I would also guess a deep bruise. Or a minor sprain inside the foot. In my first month of running in FiveFingers I overdid it and experienced something pretty similar. I hit a weirdly angled curb badly and had that weird feeling. Not immediately painful, just kinda gross like something moved that shouldn't have. Afterward it definitely started to hurt.
I had to just wait until it felt better before starting again. It took a few weeks.