M.S.
What kind of milk is he drinking now? I know this sounds simple, but is he on cow or goat dairy? Mucus and constipation are classic dairy PROTIEN allergy or intollerance symptoms. My kids have never had an ear infection and I really think it is because they were both allergic to milk and had to be on Alimentum and then Neocate Jr. to stay dairy free.
Maybe try to cut dairy and see if you see anything. Neocate is so super expensive, but Alimentum is in the store, so you could give it a try for a week and see what happens. The reduced lactose and Lactaid type milks don't work because they cut the milk sugar, but if it is the protein, these can't be altered in the same way.
I am very sorry for you frustration and problems, I hope between mamapedia and the doctor we can help you help him. Good Luck and best wishes~