Hi there,
I am also doing the Team In Training for the Tour de Tucson 109 mile bike ride. I am a Podiatrist and although I can't examine your foot, it sounds like you may have something called a Morton's Neuroma. You can google it on the internet to get more info. Your shoes may be too narrow for you?? There are lots of things that a Podiatrist can do for you to help relieve your pain. You may benefit with a good pair of custom inserts with a metatarsal pad to seperate and off-weight your met heads!! Good luck!!!
Anna