M.,
Don't know if you are already trying this, but my first (my daughter)was easier than I thought. I was worried about the night thing, thinking how in the world do I know when she is ready to go without a pullup at night. She would wake up most of the time dry, but there would be maybe one morning or two out of the week when she was wet. That went on for about a week or two and I realized that I needed to just try without the pullup. I made sure that she didn't drink anything 45min-hour before bed, I was able to shorten this a few days after going without a pullup. Made her pee RIGHT before bed (and never took I don't have to go for an answer, would make her at least try) She too, is a deep sleeper, but I put a water proof mattress on her bed and then let her go to bed. From that night on she never had an accident. And she never woke up to pee in the middle of the night. Its like her body just knew not to go.
I would say that your son is a little set back because of getting used to a pullup for a little longer than usual, but it'll work out. I'd just make sure that he isn't drinking anything an hour before bed, get him to pee before bed (if he can) and worst case scenario wake him up to pee when you go to bed. If it takes a couple of wet nights I think that his body will eventually learn.
I will say though, I'm in the process of potty training my son during the day and boys pee a lot more aften than girls. I think that their bladders are smaller and therefore they pee more often and not as much at a time. I'm finding my son drinks that same as my daughter but he is peeing 80 times a day it feels like, were she was a piece of cake to potty train! Good luck and I'm sure it will come along. If it doesn't then I would check with your doctor again to see if maybe there is something else you can do in case his bladder is still relaxing too much at night. Jennifer