Hi Jools987,
I agree that barefoot running and the newer style of deconstructed footwear to ease people into this style of running is very interesting and makes a lot of sense.

It is difficult to discuss specifics regarding ideas to assist you without knowing more details about the specifics of your self treatment. Do you work in musculo-skeletal or Sports areas of physiotherapy?

To take a wild guess I suspect that the core stability biomechanics require close attention to reduce lumbar lordosis / correct pelvic tilt and assess any side to side imbalances in muscle lengths affecting posture. It is assumed that you have not had any serious lower limb bone injuries or congenital shortening. An examination of the types of previous injuries may provide a hint to the conditions that may be common to injury causation eg Do you have other hypermobile joints (classified as the true genetic expression or part thereof) and if so a strengthening program without stretching would be necessary.
If your symptoms are suggestive of stress fracture behaviour and have been present for more than three weeks a bone scan or x-ray may be worthwhile. If the problem came on over a few days post barefoot run you may have twisted / strained some interosseous ligaments, which can present as described. Foot taping during a run may help reduce the pain, or just wait until the soft tissue heals, providing mobilisation to the structures during the process.You may benefit from a colleague or yourself providing axial traction through the affected toes whilst mobilising the joints. This technique takes a little practice but you can use yourself as a guinea pig. The area can be painful on compression forces but ease with traction mobilisation - sometimes a click is obtained at the metatarso-phalangeal head and relief follows.

Another method is to use a frozen plastic bottle to roll under your foot (across the arch) with about a third of your body weight placed on the bottle in standing. Roll the bottle back and forth for up to two minutes. The mobilisation effect of the bottle can assist both the dorsal and plantar surfaces.

As stated, I would require more detailed background and injury behaviour to be more specific. The problem may have an entirely different causation from my postulations eg neural pain via nerve entrapment or even a variant of sciatica.

Let me know if I can fine tune anything for you.

Cheers,
MrPhysio+

Obviously, if you strongly suspect a fracture, get this eliminated from your possibilities first.