Have you gotten fitted for a decent pair of running shoes? I got terrible shin splints (runs in the family) through high school and part of college, then went to a running store with my friend and spent about 3 hours talking to the local running guru. He asked me a billion questions, then grabbed a pair off the shelf (sized me just by glancing at my feet), told me to put 'em on, and then had me run around the block while he watched.

Gave me a few pointers on form, and told me to come back in a few weeks if I was having pain. I haven't gone back - I gather that the pain of being slow is one I'm going to have to live with, at least until I'm under 200 pounds.