Take a fish oil supplement, something with glucosamine, chondroitin and MSM - pretty much whatever you can find in the joint health section of a Whole Foods or GNC. I used to have pretty bad ankle problems stemming from multiple sprains during high school football, as well as achilles problems. I used to wake up every morning with my ankles/achilles so stiff that I had to walk on my heels for a few minutes before they would loosen up. I eventually fractured my ankle playing basketball, and spent 5 weeks on crutches. My right calf was pretty atrophied when I got off crutches, but I never had the same ankle problems again.
Fighting through ankle pain is a stupid suggestion. You need to give your body time to rest and heal.
Additionally - what kind of support are you getting from your footwear? Do you pronate? Not having sufficient support could be causing pain/injury as well.