The separation agreement that you signed is a binding contact. You do not have to make changes. Changes can be made if the two of you agree. If you agreement you will sign a new agreement.
If the two of you have been separated for 3 years you can file for divorce. You do not need him to agree to the divorce. You have been separated for the required amount of time in NC to file for divorce.
The only reason your separation agreement would be before a judge is if one of you filed an action regarding the terms of the agreement. The agreement can be incorporated into the divorce decree (depends on the language of the agreement). If that is the case the judge will not hold a hearing regarding the terms of the agreement. He/She will be looking to make sure it can be incorporated and the signatures were notarized.
So, you should file for divorce. Don't wait for him to do it. Don't make changes to the agreement unless that is what you want to do. He cannot force you to make changes. The agreement is binding.
This information provided is general in nature and does not create an attorney client privilege. Please consult with an attorney to get a more detailed and specific answer to your legal matter.