Believe it or not, every human being has one leg that is at least slightly (typically imperceptibly) longer than the other. And it can have an effect on our biomechanics.
The book Injury Free Running by Tom Michaud actually goes into some detail on this and how to best handle it. Typically you figure out which leg to address and wear an insert in your shoe for that leg, and it helps.
The book Injury Free Running by Tom Michaud might be worth a read in your case.