In reply to DreadyCraig: Was going to suggest changing footwear but sounds like you've got everything covered already. How about taking down the intensity of each individual day - I usually find I can go a certain amount before the skin starts rubbing off. I walk, not run but I guess it's the same principles. A couple days of going just short of my feet falling apart, and the skin starts to toughen up. I've mostly had problems on my two pinky toes since they curl under my 4th toe a bit.
I've always punctured the blister with a pin hole, drained the fluid, then left to heal maybe with a plaster or compeed. This seems to help develop calluses if the blisters have been allowed to go too far and create pain. I've never tried to preempt them.
Hope thats some help