The Ambry test that "goes all the way" as far as looking for mutations is expensive; that being said it is the best way to make a definitive genetic diagnosis.
Ambry tested according to what your doctor ordered. Many doc's order testing for only the most common mutations, not because it is less expensive perhaps but because the most common mutations are, well, more common. If this test is negative, what many doc's then fail to understand is that more extensive genetic testing might be indicated. It certainly sounds like more extensive testing is warranted in your child's case.
My daughter still doesn't have many overt lung symptoms but we are treating her lungs very proactively. Her GI symptoms were what pushed the diagnosis. Her Creon and Prevacid have absolutely made the difference in that aspect of her health. Good luck.