I had that problem in my right foot (which is 1/2 size larger than my left foot). In my previous bike shoes, my toes were in such pain after 10 miles that I had to stop, get off the bike, remove my shoe, and rub my toes for a few minutes before we could proceed. They felt like they had a hot burning band wrapped around them getting tighter and tighter.
One day I rode with a group some miles from home so I had to drive to meet them. On the way home, I stopped for dinner at El Polo Loco which often has a long drive-through line. While waiting in line in the car, I noticed that the toes on my right foot felt numb while still in the shoes. That's when I realized that they first went numb, then the numbness led to excruciating pain, which subsided as I stopped riding but returned to numbness while I was still wearing the shoe. Those shoes fit well but were very stiff.
I switched to Sidi Dominators and now I can ride many more miles before I begin to feel any pain at all, but it's NOTHING like what I had in the other shoes. The Sidis are like black leather slippers on my feet (OK, slippers with cleats).
The problem is my toes, not the shoes. My 2nd toe is longer than the big toe and I believe it gets pinched in the shoe box while riding.
All that to say........... one thing that helps a lot is to curl my toes inside the shoe every so often while riding, to encourage good circulation to the toes and prevent numbness which leads to pain.
I hope you find a good solution -- this is not uncommon and can take some experimenting with shoes or inserts, or both.



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