First, I am sorry that your child is so ill. I am a 40 yr old mom of 3, and I was diagnosed with Chiari 1 at 33 yrs old. I remember severe migraines and alot of GI illness as a child. And I was told by a couple of docs that even though most of my migraines begin as a result of the malformation, I still should be careful of other migraine triggers. My daughter is 12 now and has suffered with migraines since her toddler years. She would become very irritable and cry holding her head. I took her to a neurologist, and she is borderline Chiari. But we eliminated the more common migraine triggers from both of our diets and have seen a dramatic improvement in frequency of migraines.
If you haven't already, try to keep a food diary: write down everything he eats and drinks for 2 weeks and try to notice any patterns. MSG and tyramine are definite migraine triggers for my family. Also, storm fronts moving thru our area will put me in bed for 24 hrs.
I know it is maddening to watch your child be in pain and not be able to help, but be persistent and trust your parental instincts.