Good questions Bethany.
Hugs. I can sympathize. Thomas did lnot sleep through the night well until 18 months and still gets up a few times a week at the 4-5:30 time slot. You will survive, however hard it is. I did not think a person could go on such little sleep, but we did. I basically slept in a chair for a year when I held him. The good thing is you have a diagnosis of sorts and looking at the thread about hidden dairy should help any issues there.
I would also keep a very careful diary of foods, poop, naps, sleep, NWs, spit up and all the rest. A clear pattern should emerge after a week. You may be able to tie some things together and find the trigger. When I kept one for a month, I was amazed at the tiniest thing that set our lives on fire. I also did not link his runny noses and sneezing to foods prior to it either. If he is milk protein intol, I would consider elim of soy as well. Thomas did better with the elim of milk, but the kicker was the soy. peace began to settle in our house. The diet is hard, but it is worth it.
Also, why does he have to wean from the Neocate? I would keep it as long as he will drink it. It is so hard (trust me I know first hand, as we are losing pounds and ounces while still getting taller) to ensure good nutrition without that as a supplement.