J.M.
I have not experienced what you are and am sorry you're going through this! Few thoughts based on your post:
1) My husband's family had several children (he's one of eight) who were deemed "small" when they were young. They all ended up fine and just grew later in life. My husband entered high school at 5'2 and left 4 years later at 6'2. Granted he was the skinniest thing EVERY, but that caught up with him too.
2) Every October there is free testing done at the University of Chicago hospital to check to see if a person carries the Celiac gene/has the disease. I believe it's a blood test that can detect the liklihood of developing the disease. This may be a faster and easier way of determining if there is an allergy to gluten than through diet alone. Check out this site for more information: http://www.celiacdisease.net/testing
My grandmother was diagnosed in her late 50s with Celiac Disease and my mother was dianosed in her mid 50s with the disease. The University of Chicago hospital has one of the more advanced Celiac Disease information/programs/diagnosics/etc. in Chicago. The site is a wonderful information source.
3) Have you considered getting a nutritionist involved? They may have different recommendations for fat/calorie intake than your doctor because it's what they specialize in.
4) Either call your doctor and have another discussion and get your concerns and questions answered or get a second opinion. (I'd do both - simply to learn more about what the doctor is thinking and why he isn't more concerned, and then to present the case, your findings and your current doctor's thoughts to a new doctor.) If you don't see a pediatrition, maybe find one that specializes in growth and development. Or perhaps a pediatric gastroenterologist.
I know there are a lot of people who have great experiences with family doctors and general practicioners, but pediatritions SPECIALIZE in children. It's their only focus.
Good luck and please send an update!
Hugs,
Jen