If it turns out he has MCAS don't stress too hard (like I did), its apparently a lot more common than they originally thought In kids and infants. I was told by her immunologist that it is fairly transient and relatively benign, unlike conditions like Mastocytosis. However, even on the pediatric level, it's definitely something you don't want them to have.
Our daughters MCAS comes in the form of Cold Urticaria. This is rare (1:100,000). Her mast cells are activated when she comes in contact with cold stimulus, swimming, aircon, cold wind, ice etc..... she breaks out instantly in hives and welts. Really horrible, but I'm happy to hear immunologist believes it's something that is benign and she will hopefully outgrow. It's only the mast cells on her skin which are being activated she has no systemic issues. (lucky we live in hot Australia).
I would be interested to know if MCAS is connected to FPIES. Seems odd to me our daughter has no IGE allergies yet two very rare non-IGE allergies. I can also see a lot of other parents have kids with both of these conditions as well.
Her MCAS occurred soon after she went into shock second time with FPIES. There is a lot of good information on Pub Med regarding pathophysiological of both conditions if you are keen to read more - but it's complicated and so much is still unknown. The physical proximity between mast cells and T cells has been demonstrated in several T cell-mediated inflammatory processes but her immunologist seems to think different cell process and unrelated (but I just don't know about that! Too coincidental don't you think).
It terms of more readings I would suggest, Pub Med for all your research and learning.
Overall Health advice- I love listening to Chris Kresser (podcast and his books). Incredibly educated ,intelligent guy and a leader in functional and integrative medicine. You will soon feel helpless dealing with conventional doctors with your sons condition. A MD is great to help in an acute fpies or mast cell setting but I found they really offer no gold advice on diet or lifestyle changes to ensure overall health.. but In contrast to conventional care (which is almost entirely focused on suppressing symptoms), functional medicine eliminates symptoms by addressing the underlying cause of a problem. So I couldn't recommend this guy more!
You could also look into GAPS diets down the track to help heal his gut, and have it tailored to low histamine if you feel that's an issue.
With regards to him waking at same time at night and vomiting all flushed. Our daughter did same thing when she was younger had me so puzzled as it wasn't fpies related. Does he get really bad reflux? How rugged up is he at night?
I actually found with our daughter this issue was totally unrelated to anything and was simply from putting her to bed too rugged up in winter, she would wake upset and hot and cry - but due to bad reflux would instantly vomit. Your sons issue probably completely different .....but just thought to share.