I would recommend him going to see a infectious disease specialist, he may have a parasite, did they test for any parasites? Usually most doctors wont, due to the fact its not that common. Mold can cause a series of issues. There is tests for exposure to mold to see if you have any mold-specific antibodies. But take him to the doc or to a Infectious Disease Specialist.
I know that he sees a gastroenterologist. I do not know every test they have perform, I imagine they did over all general testing. Know of they did blood work, but unsure of bacteria in blood stream test performed. With issues with water problem in previous house and working in a hospital the range of possibilities of what it could be is large. Looking for anything odd that isn't usually tested. The hospital he worked at is a large well known student hospital, that sees alot of patients in surrounding states with special diseases and viruses. The doctors he sees is at the same hospital and just crossed. So if we could get any input of something uncommon or rare would help. Looking in any direction for help.
Sounds like there is something major going on. I am not sure, but have they checked for bacteria in his blood? Regular blood test i don't think show this and i am not sure which test is done but you could ask. I don't think by no means it would hurt. I hope you find the answer soon. He might should get a referral to go see a gastroenterologist. Hope you find an answer soon.