My son went through this. If he is upset, but you feel like he's not fully awake, that's night terrors
Check his tongue. Does it look "Geographic"? It's obvious if he does. If so, that's a Vitamin B deficiency.
Night terrors are almost always caused by food allergies or hypoglycemia.
Avoid offending foods. Try an elimination diet. Since he's on the autistic spectrum, have you considered a gf/cf diet? AutismNDI.com is a good resource to get started on how to do this. 1/3 of kids on the Spectrum are 100% food allergy responders; 1/3 are partial responders; 1/3 have no response. It doesn't cost anything to try it.
Avoid sugar or sugary foods, especially before bedtime.
Increase his animal protien in his diet.
Make sure he's getting enough minerals, especially chromium. If your doctor is willing to do a vitamin panel (its'a blood test), it might be worth it so see what's low and what's high or what's missing in his diet. It doesn't always reflect what you are giving him. Some kids on the Spectrum suck in minerals like nobody's business. My son was a big Zinc-sucker. But, each kid is biologically unique so you really ought to find a doctor who understands metabolic issues and autism, if you haven't found one already.
DAN (Defeat Autsim Now) has a list of doctors for your area.
Hang in there.
S. (read my bio)