I wonder if maybe your saddle is too high or too far forward. Those give me all kinds of trouble with my calves (which, the calf muscles operate on the feet and toes).
Have you had a fitting?
Or, maybe your feet swell while you ride, and your shoes are actually too small? Or they're too big, and your right foot is trying to grip the sole of the shoe to keep it from moving around? Most people's feet aren't exactly the same size - do you know whether your right foot is bigger or smaller than your left?