My first thought is the width of the toe box on your shoes might not be enough for you.

I suggest this because generally, Nike running shoes run narrow. Adidas shoes are generally wider (I can't wear Nike, but I can wear Adidas). Sidi's are traditionally pretty narrow, too. I can't wear them at all.

You may need a wider shoe? Can you borrow a pair from a friend to try out and see if that helps with the pain? I wear only Specialized shoes because the width is just right for my feet.

Of course, my foot pain is different than what you describe, so this might not be it at all. Helpful, aren't I?