If you were fine for two hours, it may not be the size. Does your toe feel jammed? or back of your feet along the achiles heel rubbing the back of the shoe? if not then its not the size.

Or did you clamp down the closure/snaps too tight? did you try loosening them so you foot has bit of wiggle room on top of your feet above the arch. If you clamped down hard, this can cause quite a bit of discomfort.

Cleat position in relation to the ball of your foot does matter. It may not be positioned right.

Another possibility from the sound of things is that the sole of your shoe may not be stiff enough or you don't have enough padding under the ball of your feet.

I'm just shooting in the dark right now. See what others have to say. I do sympethize with you about a painful shoes. It sure takes the fun out of the sport.

smilingcat