M.H.
HI Michelle,
Have you ever used chiropractic care? I started using a principled upper cervical chiropractor when my oldest girl was having febrile seizures/ear infections and my second went straight to the chiropractor's office from the hospital...It has done wonders for our overall health. Neck and head pain, not only is bad, but can lead to other issues as well. If you don't have one you can go to ucspine.com and find one in your area. When you interview them, just like a regular physician, ask them to explain how chiropractic care can improve the immune system. If they can't, find another one but most on this site are great doctors. Most are great diagnosticians as well.
It's completely possible that he slept in a funny position and he simply needs his vertabrae to get back to where they are supposed to be. A proper spinal alignment is important to the entire body functioning properly.
Hope I helped!
M.