I got custom Orthotics from the orthopedist, (expensive -- $400 - but covered by insurance) which I put in my regular shoes and the bike shoes. They helped by about 50%.

I found no heel pain after a 30 mile ride Saturday, but some from a much shorter ride Tuesday. Who knows? Walking on concrete sidewalks, which I do a lot here in Brooklyn, seems to aggrivate the heel the most. Stretching does seem to really help, so I do extra after a ride.