Even though my gender confusion is perplexing me at this time, I don't percieve it as a "problem", but rather a personality characteristic that is being exposed to the light. It is not like depression where there is a collection of symptoms that overlay experience. It is more like the an aspect of the "me" that has the experience.

Your son may have some feminine characteristics. These are not his problems. How other people treat him could be. Rather, how people WILL treat him, WILL be a problem. Reassure him that there a lot of jerks in the world, and they may make the loudest noise, but MOST people are decent and understanding. As time goes by he will be able to sort out who is near enough to him to minimize the conflicts.