I'm so sad reading your email! How utterly frustrating to have no answers that make sense and watching your son lose weight continually. I have three suggestions.
When they checked for allergies, did they check for Celiac Disease? I know you have reduced wheat, but it could possibly be the gluten that is in all kinds of grain and is an additive in most processed food. It would be worth it to find out, and there are plenty of gluten-free foods on the market now so that he doesn't feel left out. I've also read that 1 in every 133 people has a gluten intolerance, but most don't know it.
My other comment is that the woman that mentioned ProBiotics makes a very good point. ProBiotics really help the body to digest the nutrients in food if the system is having trouble. We were recently on antibiotics for strep throat and all of us ended up with horrible stomach aches and indigestion. We all got onto the ProBiotics and within a day felt normal. They make ProBiotics for kids that taste good. Be sure to get the kind that is refrigerated.
My third thought is that western medicine has always had shortcomings in curing chronic problems. You might consider going to a Naturopath. Over the last 10 years I have gone to both a medical doctor and a Naturopath. Consistently the Naturopath is able to get to the source of my problem and heal me, where the medical doctor only prescribes medicine to deal with the symptoms. Naturopaths have to go through a rigorous program that involves all of the premed classes a medical doctor goes through, so they know human anatomy and physiology as well as any MD.
I hope this helps.