What are the steps I need to take to gain custody of my 2-year-old who lives with me even though I am not the custodial parent?

I am unclear if you and the mother of the child were married and she has custody pursuant to a custody order.  When you say full custody I assume that you mean she is supposed to have physical custody and she has the right to make the decisions necessary for him.  If the answer is yes to both of my assumptions then you need to go to court to modify the order and gain physical custody as well as the right to make the necessary medical decisions. 

If there was no marriage but there is still an order then you need to do the same.  If there was no marriage and is no order then you need to establish paternity and bring an action to gain custody of your son and the right to make medical decision on his behalf.  The best interests of the child are the general standards used by the court.  You will most likely have to bring his medical condition to the court's attention and possibly challenge her fitness as his guardian.  Good luck.