The reflux and the antibiotics he would have been on for the pneumonia would actually make me more inclined to think it's a yeast issue. Removing the yeast alone wont make a huge difference as there would already be overgrowth there. You need to stop feeding that yeast as well as not adding more yeast, so that is why gluten and cane sugar have to be removed because they feed the already existing yeast.

I could be wrong but I doubt the RCH tests would have tested for an intolerance. There is a difference between an intolerance and an allergy. An allergy is an immune response, while an intolerance is a chemical reaction therefore they require different tests. Also, you don't have to be intolerant of yeast to have an overgrowth.