It can take up to 2 weeks for the proteins to completely leave his system once you've eliminated dairy - how long has he been off of it? And is he still sick?
Dylan's sleep was absolute garbage while we were getting very thing sorted. If you look back to my very first post on the forum it was asking about pu/pd because he was waking every 45m-1h all night long
It was horrible. His sleep got a bit better when we discovered his dairy allergy and I eliminated (ebf) but he still woke frequently. In retrospect, that was due to the fact that he had other allergies and I was still eating those
his sleep did settle around 16mo when we did the testing, I was breastfeeding much less, and we eliminated everything. But even then it took a few weeks for the proteins to get out of his system and for us to wean the props that we had been using (he wasn't waking from discomfort anymore, but waking from habit to eat a cuddle, for example).