Why is my 4 year old waking in the middle of the night?

My son, who is four, is a very good sleeper. We have never had problems with him waking up or falling asleep. He is developmentally delayed, has a shunt for hydrocephalus. He also suffers from chiari I malformation. I had him at the emergency room last evening because I was scared that it might be sleep apnea or something neurological, which I think the two are still likely. They said he had an ear infection. This boy has had over 40 ear infections and his sleep was never affected like this. No changes in his days. Still naps everyday. Goes to bed around 8:30, then roughly two hours later he is crying, but sleeping. If I rub his back he stops. He is moving around a lot- changing his positioning. I did have him with me on the couch a few times and he did stop breathing for 5-7 seconds and then gasped. He has been snoring and breathing with his mouth open. This would all lead me to believe it's apnea. After 2-3 am he seems to sleep until morning. Any suggestions?