I really feel for you. You are trying so hard to do everything right now and it's just not possible. After a point you just get so stressed and overwhelmed you can't make any decisions and everything gets too hard.
My advice, for what it's worth, is to try the new Crohn's medication and then just let everything else go for a while. I understand it feels impossible to just step back for a minute, but you need to let yourself be in a calmer state, for your son's sake and for yours. I don't mean to come across as lecturing you. I'm just worried about how frantic you are feeling and how much that's exhausting you.
As
@hapl808 says, this disease is a marathon not a sprint. Resting up is important to finish the race. The hard truth about healthcare is that it works (mostly) in probabilities, not sure things. The certain answers you seek don't exist, but you can sure torment yourself trying to find them. This is one of those times when you have to make a decision with imperfect information. I can see how badly you want to make the right decision and help your son and you're really doing a good job. But there is no perfect information here, so you have to let that go for the sake of our health and sanity.
When you're exhausted it feels like you need to do everything at once, and you just don't. You get too overwhelmed to prioritize. You don't have to think about the antidepressant right now, you don't have to think about the sleep study right now, you don't have to call Dr. Rowe right now, you can put the provigil right out of mind. Just focus on getting the new Crohn's med and let that settle. Once you try that and see your son improve (or nothing happens at all) then you can regroup. I have the feeling that medication is what's preying on your mind the most and also the feeling that has the most potential to be helpful of everything you have mentioned to us.
OK, end of lecture. Take care. I'm thinking of you.