I'm having some minor (uncomfortable) pain in the outside top of my right foot (think around the inferior peroneal retinaculum or the inferior extensor retinaculum near the external malleolus). It started out just noticeable for a bit after my run, but as of today it's a little tender even to walk. I have changed shoes in the past few weeks to start running "barefoot" (with Vibram Bikila LS). Is it normal to have some foot pain like this until my feet fully adjust to the new shoes? It isn't preventing me from doing anything yet, it's just mightily uncomfortable.
If you could go below all the fascia and muscle in that picture, you could see the ligaments that connect the bones:
The anterior talofibular ligament lies in the area you point to in your image. According to Wikipedia this is "the most commonly sprained ligament," so there's a good chance that's your problem. This article can give you more info about the signs and symptoms of an ankle sprain and what you should do about it.
Vibrams have zero ankle support so you rely completely on your own muscles for stability: great for building strength, but you're much more likely to get injured. Make sure you take enough rest time to let your injury recover, then I would suggest working up to running barefoot to prevent overuse injuries (sometimes use running shoes, sometimes use vibrams). Also, consider doing ankle strengthening exercises.
If you were already an avid runner before you started the barefoot thing, you have to remember that barefoot running is completely different. If you run 5 miles a day in tennis shoes, you will most likely get injured if you all of the sudden start running in vibrams. You have trained your feet to work with a standard support system your entire life, and can not expect them to be able to hold up when they're suddenly stripped of all that support.
You probably have an injury that will need some time to heal meaning stop wearing the vibrams until the pain stops. In the mean time, use an anti-inflammatory, ice your foot regularly, and of the pain persists, go to your doctor, and consider seeing a physical therapist.
I agree that ankle exercises are a very good idea. You could get a balance board for example.
Once you feel that the problem is alleviated, you can restart your barefoot running program, but you should really limit the amount of time you spend running in the vibrams initially, and increase the time at a very slow rate. Your connective tissues do not increase in strength as readily as your muscles do, so give your body plenty of time to adjust.
I know from personal experience that you can do major damage to your feet and ankles running when it doesn't feel that bad at the time. Don't just go out for a run, and decide you feel pretty good that day so you do your long run in the vibrams even though it's just your second week in them. It's not a good idea.
I'd suggest using the vibrams 2 to 3 times a week for easy runs only for an entire month. Then start using them for an additional run each week maybe doing intervals or some other type of speed work. Don't be in a hurry to get rid of your running shoes.
Lastly, if your feet aren't structurally sound, vibrams might just not be an option for you, so be open to that possibility.