A neuroma can mimic those symptoms – especially starting in the ball of foot. It is likely irritation from hypermobility in the forefoot and metatarsal heads squishing nerves. If it improves with massage, it is likely this.
Another possibility, though much more rare, could be chronic exertional compartment syndrome. Though more common on leg, this can appear in foot. If the pain is resolved completely when you stop running – this may be the case.
Lastly, it can be a stress fracture if it is red & swollen.