You have not tried everything. Try some Flow bindings as a last resort. Traditional straps just might not be the best bet for you foot pains. This is the reason I use Flow bindings. Prolonged riding in traditional straps give me discomfort in my feet as well. I'm not entirely sure if it will help you since your pain is in the balls of your feet, but hey... you've pretty much exhausted every other option.
Are you doing a lot of presses? I noticed that the more I do tail presses and butters, the more my feet hurt. You just might need to go mellow for a while. You could also get it checked. Another alternative would be to down a couple of Ibuprofen pills before you shred. It will help decrease the pain.
Actually, your last resort would be to try a Burton ICS board with EST bindings. There is no hard plastic on the footbeds of those bindings. It is all dampening cushion.