From everything you’ve said, it sounds like central precocious puberty.  This can be triggered when a child with CAH has been under-treated for a long period of time, THEN brought under good control (how you have described your son). 

I am glad your doctor is concerned, but children with CAH are generally brought to the ER because they are showing signs of adrenal crisis.  Not because they are showing signs of increased penis size and pubic hair.  As well intentioned as your doctor might be, I don’t think he is handling things the way most good endos would.