Can it be Gastritis?

I have a two year old son that will wake up complaining in the middle of the night, will vomit once and goes back to sleep.  We treated  him for acid reflux with zantac and the vomiting stopped for a while but started with a nasty cough and fever. Had many tests done, blood, x-rays, stool and urine tests and nothing to be really concerned about. Just when the fever stopped he started vomiting once at night again. Dr. says is probably just a virus that will go way. I am almost sure the fever will come back. He also has greenish stools with mucus and smellier than normal and after the fever was gone some type of mild rash in his back and tummy. We are taking him to see a gastroenterologist next week to get his opinion.