I am not a doctor so I cannot diagnose your condition. I encourage you to read about the symptoms of Gastroesophageal Reflux Disease on this site for further information about symptoms. Many patients with GERD have a sour taste in the mouth and cough/gag in the morning. Reflux and sleep don't mix for many people.
While GERD is more commonly associated with heartburn and chest pain, some patients do have stomach aches or stomach pains.
There are many possible reasons for your symptoms from other health conditions, medications and diet. Only a doctor can sort out all of the reasons for your symptoms.
I hope you will work with your doctor to find out why you have such a unpleasant wake up call.