Not sure if this helps, but I have low arches, particularly on the only foot that gives me discomfort (only while running). Mine is outside top about where anke and foot join.....and x-rays show that I do not have the extra cushioning where the leg (Fibula I think) bone meets the foot, in other words there is sort of a grinding that goes on.
Stability shoes such as the Nike Air Structure Triax or Mizuno Wave Alchemy are musts for me. Also running on right side of road (it is my right foot) seems to help as well. I take glucosamine daily and it is hardly noticeable until I run out of the stuff....so I think it helps as well.