First things first. Get your running gait assessed by someone who knows what they're doing. Someone like Zig at Motion DNA or I'm sure there's some running addiction group (
) that knows who to see.
It sounds like you have pretty large kinetic chain issue involving at minimum the hip and trickling downward. the lower extremity fatigue pattern may be the indicator (sounds like you're staying in pronation too long on the affected side)
That said, you may have a bit of a deep peroneal nerve issue (this goes along with hip, ITBand, hamstring, and some other fascial issues). Have someone test your dorsiflexion manually and compare sides. Use a pretty decent level of force to test it and use a sustained force of about 10 seconds or so because it'll take a little time for the fatigue to kick in.
If you test weak or it feels like it takes a whole lot of effort to resist, go see an ART doc for a quick fix. If that doesn't work, follow up with your doc and get it checked.
Bill