When I go on a longish ride (for me) - 4 or 5 hours, I get an excruciating pain in the middle and "ring" toes on my left foot. The pain usually starts after an hour or so, but doesn't get excruciating for another 3 or 4 hours.
I doubt it's the shoes and/or fit. I get the same pain on my 1985 Tequesta with sneakers/cages and my 2012 Motobecane Immortal Force with Ultegra clipless pedals and Shimano R087 shoes.
I am trying to figure out if I am clenching my toes as I pedal or something like that.