Has he gotten any sort of physical therapy- or a comprehensive evaluation by an advanced PT, DC or osteopath (DO)?
These people study more of how the whole body works together , more than general MDs usually do.

If no one has a referral for your area , searching out experts in the fields I mentioned for your area might be the next step.

I hope someone can help you with some good names for Stockton, CA area.

Other thoughts--
His neck muscles could be in spasms - that could contribute to the headaches. ( muscles would be hard & not pliable like a normal muscle)
Trigger points could be a factor if there are small extremely sore spots/knots in the muscles.
Possibly an expert upper cervical chiropractor would be of help. The c1 c2 could have gotten misaligned and that can upset many things in the whole body alignment.
Also, possible pinching of the vertebral artery by the vertebra, or muscles in spasm pulling on things can contribute to headaches.