I was pretty startled to learn how loose I could leave my shoes and still make good power. If you feel like your feet are moving around in your shoes, it may be an indicator your pedaling form could use a little focus. (No offense intended--I had terrible pedaling form two years ago and didn't know it, but I've been working on it and my feet (& @$$) almost never hurt anymore.)
Keeping your toenails trimmed?
What kind of shoes do you currently have and how many different kinds have you owned in the past? Toughing it out is a lousy option, IMO.
I was also surprised to learn that you don't have to get smaller sized shoes, even with clipless. I went up half a Euro size on the recommendation of a bikefitter and my feet have been plenty cosey, even in my plastic clown shoes.