Hi E.,
Everything in your body relates to the other parts. They are all connected...a bad digestive disorder can cause kidney stones, poor nutrition can cause bone loss AND acne, scoliosis can be the cause of gout....I could go on and on. It sounds like your little one has a weak immune system and any nutrition he is getting is not being absorbed properly. Nutrition is the key to most problems. Nutrition builds the body strong so it can manage or fight off anything that is not normal...like an ear infection or acid reflux. If the digestive system, the spinal column and yes, the mouth, are in good health, most everything else will be too.
The meds he was on may fix a problem temporarily but antacids will cause a rebound effect and the next time the reflux comes, it will come with a vengence. Stomachs are meant to contain stomach acid to digest food. If the acid is not there, the food does not digest (it rots, ferments, etc) and will cause the reflux. the stomach doesn't just start doing what is supposed to by itself. It has been abruptly stopped and it will stay stopped until. It also means the food is not digesting and the nutrition is being destroyed. The ear infections come because his body does not have enough strength to fight them off.
I lived with digestive issues most of my life, and all of my childhood, and if one doctor had told me how to eat instead of medicating me I would have been as healthy then as I am now. I KNOW the doctors still prescribe the same way they did when I was little and it appalls me that they have not learned from their mistakes. I know your little one needs an absorbable multivitamin (I know a kids chewable that is guaranteed to absorb) and he needs to be eating a lot of fiber. Milk is not an evil thing unless there is a condition that it exacerbates like your son's. I would remove all dairy from his diet. Chiropractic care can jumpstart an immune system to working right. If you don't have one you trust that understands the immune system, go to upspine.com and find one in your area. Detoxing his body and your home will help as well. anything that will give his body relief will start the healing process.
If you have any questions, feel free to ask. I'll be glad to help.
M.