You sound like you’ve done the rounds, so you probably know that GI issues often cause vitamin and mineral deficiencies. Tell me does he remember to take a B vitamin supplement daily ? I think vitamin D deficiency may have been linked to migraines too.
Is he hypermobile by any chance ? It could be his head position aggravating things – chin down is bad, head pushed forwards by pillow is bad too. Have you tried him with a ‘cushtie’ type horseshoe-shaped neck cushion, for when he’s sat relaxing. I recommend that a fastener of some sort be sewn to the front ends, so it can be closed to form a circle around the neck, it gives better head support that way.