I have a problem very similar sounding to what you mention. It's the tendons. It can take up to 12 weeks, yup you heard right, 12 weeks for tendons to recover from injury.
I would see a physio if I were you. They may be able to tell you for sure. Could be a stress fracture, or at least an injury that could result in a stress fracture. Resting for at least 4 weeks is your best option.
agree that the cause is most likely to be running on the road in minimal shoes at a faster pace than normal.
I would suggest investing in a cheap pair of Nike free's or free run for the road or for now. The free run have far more support while allowing the muscles in you feet to strengthen.
For now xtrain. Swim and cycle. do core work and free weights. See the fizzy, you may be able to strap your foot to minimise pain and any possible further damage.