This may not be the right thing for everyone to do,but if it was me,this is what I would try Given that your son is wide awake after the diaper change, I would slather on an ton of desitin (or whatever diaper rash ointment you use) and don't change his diaper right away. If he is going through a stage of having longer p.d. time, maybe he will come out of it. It sounds like maybe b/c he is upset during p.d. he is having the bm. Since it is taking you an hour to get him down and he doesn't poop till after that hour, I would leave him w/ the dirty diaper. Does he wake any other times during the night in which you feed him? You could change him at the next waking before you feed.
Once your lo breaks the habits of night wakings, he won't be upset and may not have a bowel mvmt. By not changing him right away, at least you will not have gone through the hour of p.d. for nothing and he will learn to sleep through that waking. I know that sometimes my dd will poop during a BF at a night waking and I hate to leave it, but I will b/c I know that changing her is so stimulating. I have gotten her past the point where I have to BF her back to sleep, but still, changing her wakes her too much. With as much Desitin as I put on her....she has never gotten a rash from the times I have let her sleep a while in it. Yuck...but it worked for my dd.
Just a thought