Sounds to me like your child has asthma. I strongly suggest taking him/her to a pulmonologist or an allergist. They can do some simple tests to see if they have asthma. Do it soon too, asthma is a very serious condition. The stomach aches could be from the flonase or Cingular.
Please see an allergist, not just the pediatrician. Your son may have allergies, but he may also have asthma. Sometimes it's called "reactive airway disease" or "cough variant asthma" when the main symptom is cough and not wheezing. My daughters both have this, as well as allergies. They get a cold and all they do is cough. A steroid inhaler with spacer and/or a nebulizer with albuterol may help stop this cough if there is an asthma compenent.
Does he cough at night, while sleeping? That's an important thing to tell the doctor. If you or anyone else in your home smokes, it's important not to smoke in the house anymore, or in the car with your son.
The stomach aches may be reflux as the doctor suggests. Ask the pediatrician about reflux and what to use to control acid and see if it gets better. If it's still bad, you may need a GI doc.
A previous ped didn't think my girls had asthma because they didn't wheeze. She was wrong and we got a new ped. Asthma does not necessary have wheezing or "attacks" with shortness of breath. Here's a Mayo Clinic link where you can read more: http://www.mayoclinic.com/health/childhood-asthma/DS00849/DSECTION=2
my son was diognost with asthma at age of 2 he had some similar simptons constant coughing and runny nose also stomach pains due to the constant coughing also very tired all time do to shortness of breathe started as alergies and progressed into asthma
Sounds like your son may have gastroesophageal reflux disease (GERD). His stomach pain may be a sign of this and the cause of his respiratory symptoms. You should discuss the possibility of this diagnosis, with his doctor, and request appropriate testing.