Here's what I would try. Take him out for a walk and a pee at 1030, for about a half hour. Then, put him in the crate and leave him be. No out again at 1am. Come in through a different door where he can't see you. My thinking is that he hasn't been taught a full night's sleep, and sees everything as naps. Do this for a week (or more?) consistently, while ignoring the barking completely until 6 am. Get some earplugs.
Don't responde to his barking in the morning.
I haven't had to do this, but it is what I would try. Oh yeah, no water after 9 if you walk him and pee him at 1030.