I had a similar problem with my feet about a mile into my rides. I tried everything from a change in seats, inserts, pads on the ball of my feet, different shoes, different socks, heighth of my seat etc. I talked with a mechanic from the local bike shop and he suggested biking sandals. I tried regular sandals and then went with bicycling sandals with spd clipless pedals. I still have some discomfort but I was able to ride Ragbrai (a 500 mile tour across Iowa) this past week without any major difficulty. With the sandals you are able to flex your feet when they start hurting which seems to help. Sandals were everywhere on the ragbrai ride. I am so happy with my pedals and my sandals I am contemplating another pair of sandals just to have a spare.