I see that someone has responded to your post on the other Training BB with some ideas. I too experienced some ball of foot pain towards the end of my last race. I think it was from having been running downhill for several miles. It wasnt what I would consider really bad but it, along with sore quads, did slow me down some.
In training for my next race, I tried putting Gel Ball-of-Foot cushions underneath my insoles (the original ones). I havent had any ball-of-foot pain since but I dont like how the gel pads seem to move somewhat during my long runs. Been looking at the Sorbothane Ultra Soles but havent yet tried them. If you find a good insole for the ball of the foot, please tell me.