You said what I was thinking, it sounds like he is carrying some sort of virus, most likely hhv. Have you had a viral panel ran yet? Immune suppressing virus’s create the perfect immune conditions for a fungal overgrowth also.
It might be worth it to check out the methylation symptoms/conditions page too. Theres a link to it in one of the stickied pages. Alot of toddlers/children with those types of issues have problems in that area of the physiology.