It sounds like you are doing all you are supposed to do re the crate. Have you tried added any of your clothing as perhaps he has become more attached to you now that he has started to forget his mother and litter and is now missing you at night instead. The other thing we did was really try and wear Biscuit out before he went to bed and that seemed to work well. We tried to have him wide awake for at least 1 hour before bed.