I'm so glad that your son is with you. And that your w acknowledges that he is doing well being with you. I hate encouraging the legal process on these kinds of things. But, I think it would be good for you to file for a legal separation. It's not as "final" as a divorce, but it will set some guidelines for your son. Imagine the devastation of your wife deciding for whatever reason that she wants him back. With nothing legal in place, she can come and get him with no notice.
On the lighter side, you are awesome!
Me 36 Husband 35 D5 S2 separated: 10/29/07-present Served divorce papers 1/22/09 "When the world gives out beneath your feet, it is time to learn how to fly."