I was awarded sole custody of my 3 year old son after searching for him for 2 years and neglect charges were filed against the mother. I am married now with a child on the way. How do I go about adding my name to his birth certificate ( I have an order of filtration) as well as changing his last name to mine when the birth mother refuses consent.

If you were awarded sole legal custody, go back to the court that awarded custody and ask they they order a new birth certificate issued.