You could start by taking your son to a pediatrician who could explain the problems that may have resulted caused by his infant surgery as he grew. The Dr. might refer you to a gastroeterologist, a specialist in intestinal problems.
In the meantime it is possible that doing herbal parasite programs, something mild such as Dr. Clark's 18 day program or Clarkia in doses appropriate for his weight might get some of the congestion out of his small intestine if he has intestinal parasites. Your Dr. could order a Metametrix Lab enteric effects panel and that might show some parasites and intestinal imbalances.
I don't think that doing Liver Flushes before you find out more would be a good idea.