Swetha, I'm sorry to be so late in replying. I went out of town for several days and am still catching up! I agree with Chemar, that you have done an amazing number of interventions. You are observant and have what it takes to make real progress. In fact, it sounds like you already have. It's great you are cutting out sugars and reducing dairy. It can be hard to know what foods might be involved without trial and error--unless something becomes obvious. Maybe the naturopath could help you with that, if you see one.
You mentioned you were starting the waring of eyeglasses back up, thinking it might have had something to do with the symptoms. Have you seen a change? There could be visual component, especially since he had tics when reading and watching TV (this is not uncommon.)
You mentioned dust allergy -- have you had a chance to make the bedroom dust-free? (article) A good air purifier in the bedroom can often make a difference. Could it be possible he also has other sensitivities that you are not aware of.--like to mold?
What is his current "baseline" of tics -- how would you describe the current level to the pre-trip level of tics, before the explosion?
A lot of us can totally relate to him letting the tics out after school! It can be distressing to watch, as a parent. Hopefully as tics keep settling down, he won't have to focus on holding them in.
You asked about stool testing, that can be helpful for identifying candida as well as bacteria, viruses, or parasites. Does he have digestive problems?
Please think about chemical exposures in the home or at school, Swetha. Do you have any scented products at home? Air fresheners or incense? And what about scented laundry and cleaning products? You may have seen enough on the site to have already made changes there. This is an area that is often overlooked as it is natural to focus on food and supplements. Similarly, there could be something at school that he is reacting to.
We hope you will keep filling us in on progress. I'm not planning to travel again for a while and will keep an eye on this!