i've sprained my left ankle three times. i did rehab exercises for it the first time, and that was the worst of the sprains. can't remember them offhand.
anyways, from my experiences...
first, get a good ankle brace to wear until it feels better when running. i bought one that laces up and has straps that wrap under your heel and then velcro'd to the side, it gave great support.
second, make sure you wear good shoes (both for running and daily use) with good arch support.
finally, try doing some exercises for it...
http://www.southhillsortho.com/anklerehab.html
i've found that my ankle never truely 'unswelled.' it's always been a tiny bit bigger than the other, minorly noticably swollen, since the first sprain. the extra fluid could also contribute to some ofthe pain you feel.