I have the opposite problem. My daughter is celiac, and only one MD and my naturopath agree that she is celiac. HOwever, the results show for themselves. When she's off it, she's a different child, digestion and eating are much better, and her brain is fully functioning instead of being shut down.
My advice would be, take those things out of her diet that the naturopath recommended. Food allergies don't always show up when expected. For example, I could eat dairy then have a migraine without fail 24 hours later. You cannot tell how long it takes for a food allergy to really manifest in someone's body.
See what happens when they are taken out of the diet. It has to be taken out at least 4 days. Some doctors recommend two weeks. If there is a change for the better, then you know bingo, that's right. If there's not, maybe the test scores got mixed up and try the test again, or a different test to confirm. You can try taking out dairy for 4 days, for example, then take out peanuts and wheat for 4 days. The other thing about food allergies, if they are not celiac (which is the inability to process wheat gluten - a permanent condition) sometimes there comes a time where the food allergy is no longer there. So this is not necessarily a permanent condition.
My naturopath worked with the standard Paclabs and other labs that medical doctors use. Maybe she can get alternative tests there to confirm. However, food allergies can be so serious as to cause autism, so I wouldn't play around with this.
By the way, you can make gluten-free bread that tastes pretty good - Pamela's Baking mix in the bread maker tastes just as good as gluten bread. Places like PCC and Whole Foods Natural Markets have gluten free produce and also recipe books that help with avoiding allergens.