It sounds as though it's just fatigue from lack of support. Try some footbeds.
I use sidas con'formable which, while fully custom, are very cheap (less than USD100). For me, it means no more sore feet, no hotspots and no numb toes, no matter how long the rides.
http://www.sidas.com/
There are even cheaper step in options available that may work just as well too. I use green superfeet insoles in my hiking boots but that's mainly to prevent blisters.
http://www.superfeet.com/