This is a more common problem than you think. I can almost gaurantee that your biggest problem is due to the wrong shoe. There are many articles in Kickrunners and discussions in other forums of how to pick out the correct shoe for your type foot and gate. You'll need to determine if you are pronate, nuetral, or (I forget the other term). The best thing you can do for yourself is go to a reputable running store (Some Dick's Sporting goods stores have proficient employees to help you). Most of these stores have a machine that will tell you the type runners foot you have. Then, buy the shoe that best fits your needs.
Another thing to watch out for is how you run. Running form becomes more and more crucial the more distance you start to put on. DO NOT RUN ON YOUR HEELS. You should be touching first on the balls of your feet. This makes your ankles act as shock absorbers. If you run on your heels, in time, there will be problems.
Slow down, get your running form perfected. Many runners (especially Soldiers) tend to go to fast out the starting gate. You will gain more out of slow easy runs. You should be able to carry on a conversation as you run. Speed training will come, first get your mechanincs correct and get your body use to the mechanics. Even when you add speed training to your run, it is less frequent than what you think. When I am at my full running capacity, I'll add speed training once every other week. Then build it to once every week. I don't do any more than that. The rest of my runs are at a slow steady pace for distance (although, I do add Fartleks in every once in awile).
Do some research on your own around this site. You can get a lot of info. Also, being that you are already going through some pain, you should get a physicians opinion. Make sure there is no big damage.