It is highly unlikely that the foot pain and the headaches are related. Lower back pain and foot/leg pain are usually related.
I would suggest a consultation with a neurologist for the severe headaches.
As far as his feet go, runners often need extra shock absorbtion. He should also replace his shoes often (every three months). If this doesn't work, he should be evaluated by a foot specialist and see if a custom orthotic would help.
Good luck to you,