Nerun,
I agree with Bobolink about the shoes an would go one further in the stretching department. If you have a biomechanical problem that is causing the pains you can always try a specialist, but before you do I would make sure its not just caused by restrictions in other parts of your body. What happens in this case is that in order to compensate you end up working the areas that are moving more putting undue wear and tear on them - in your case probably your ankles. The first step to freeing up any restrictions will be to increase your flexibility. Therefore I would recomend that you sort your self out a 20-30 minute flexibility program that you do on your rest days as well as stretching after your runs.
Hope this is some help
Jim