Wouldn't it be nice if they could just tell us!
Has the dose been adjusted for weight gain recently? I don't know a lot about the various medications - that may be a question for the CRC board.
How long since you started to re-introduce the cows milk? The damage to the gut takes a while to progress to symptoms of mucous and blood in the poo, I'd reckon, since he's likely healed up by now, no? I know with DS, it took a week or so before his gut healed but it took probably 6 weeks of damage to his gut before he was obviously symptomatic.
Hmmm... if it were me, I'd probably stop the milk and see if it makes a difference - are the night wakings worse since you started it though?
Hugs xx Wish I could wave a magic wand for you to all get some sleep!