My 14 month old son is now on methadone (.4ml) 2x's a day for pain due to epidermolysis bullosa. how will this affect him in the long run?

Really no data: The only data on treating infants with methadone is in babies born to mom's who are on opiates, which is really a different population, with different problems. Most of those mom's also smoked through pregnancy, had lower birth weight babies, many had other psychosocial issues, as well as other drug/alcohol use. The good news is that in those babies, despite early delays, development ok at 3 y/o.

Need expert program: This is a chronic disease with a number of complications. He support from pediatrics, dermatology, nutritionists and a host of support services, usually available at an academic or "tertiary" facility. Also, the Dystrophic Epidermolysis Bullosa Research Organization and other support groups may be helpful