Do your toes overlap only in the winter? What is the temperature when this happens? Have you noticed if your toes have turned color at these times? This is by no means a diagnosis, but it sounds like the pain could be reduced circulation triggered by the cold. I suggest you see a doctor.

There are a few things that are very important such as:
-keep the toes separated, even with lambs wool
-keep the feet as warm as possible (avoiding cold)
To cycle then, use every trick in the book:
-2 chemical Toe Warmer packs per foot-1 above and 1 below your toes.
-sock liner with winter sock over (all breathable)
-winter cycling boots or neoprene boot shoe cover
-legs should have 2 layers of warmth as well