I'm glad to hear you found a knowledgeable GI doc to work with. It sounds like he will be looking at things from a different direction. That's a good thing.
I was recently worked up to see if I have autoimmune issues, because my allergies are so bad, and are not all that responsive to all the treatment I'm having.
Have you ever tried taking probiotics? The allergy NP I saw said that there is a lot of evidence that they not only help your gut, but can also help alleviate allergy and inflammation in other parts of the body.
I just started them, and I know it's a long-term fix, but they can't hurt. It seems that there is some evidence that gastroparesis can create an imbalance in the intestinal flora. Also, there is pretty good evidence that everyone in modern society has developed imbalance.
I don't know if they will do any good, but I figure they can't hurt, so I'm taking them.
Again, glad to hear that you are on your way to finding answers.