I'm flat footed and suffered the same sort of pain. Also Achilles' tendon pain from running. Tried all sorts of arch supports and insoles and although eased it during normal day walking, didn't do much for running.
Getting desperate for a remedy, I tried barefoot running, which started off with me just whipping my trainers off for a bit and then doing small distances, building up gradually.
I now run in minimals all the time whilst still have supports in some of my daily shoes. I'm trying to ease my foot out of supports totally.
I've felt my feet get stronger from minimal running and I also add in other exercises, such as picking up balls with my feet and doing lots of calf exercises.
Not trying to convert you into minimal, but so far it's working for me. I've just completed Hellrunner and found the whole run comfortable on my legs and feet.
The more I've been reading up on orthotics, the more I'm convinced they make your feet weaker and more prone to aches and pains.
I'd definitely recommend giving it a go, it was the price of orthotics that made me !