My daughter had weight gaining issues... Long story short: Her pediatrician told me to boost her dairy fat. A quote from her, "ice cream, ice cream, ice cream! I don't care about the sugar". I started cooking all her food in butter, butter on all her noodles and toast (even made mac & cheese with creme frais and cream--OMG it was yummy! So fattening!). Melted cheese on all her bread and vegetables...
Did she gain weight? No.
Turns out, she is allergic to cows milk/diary... No wonder she didn't gain any weight--her body couldn't fully digest it; the cows milk protein was interfering with the absorption of all other foods.
Have you done a food allergy test on him? I'm referring to the skin prick test, not the blood test (my daughter's blood test came back Indicating a high white blood cell count, but didn't point to a food allergy; only the skin prick test was able to confirm it). If your son is not gaining weight, I recommend you investigate whether he has a food allergy that is inhibiting the absorption of nutrients in his intestines. I know, it seems like such a simple explanation, considering the doctors have already done big scary tests... I say this because that's what they did to her too... Heart scan, immunology tests, CF was on the horizon (but we got the skin prick test first). It was all due to a food allergy. Once we eliminated all traces of that food from her diet, she started to put on weight.