looks like I missed this one, sorry. I would love to help you out. the first thing that comes to mind is that your shoes are too small and/or they are laced too tightly. I wear a full size larger shoes than street shoes (and my montrails/trail runners are a size and a half larger). when your foot hits the ground, it needs some space to spread! make sure when you buy those cushion-y shoes, the shoe salesperson puts you on one of those old-fashioned measuring devices (in standing, not sitting). if they don’t have one, or don’t seem to know how to use it, walk, no, run out of the store.
it’s a problem I have seen again and again with women and running shoes. for some reason, shoe stores forget that we need our feet to function, not just look good.
if this doesn’t solve the problem, let me know!