You can never truly protect a child from stupid remarks and guilt trips offered by a selfish parent. A court order will not change who the person is, but will only attempt to limit the undesired behavior. If specific language is added to the court order prohibiting such behavior and she still does it, then your recourse would be to file a petition for contempt in which you ask the judge to fine her, make her pay your lawyer fees, or put her in jail. However, in custody cases judges often do not go to such extremes and instead they will order family therapy, co-parenting counseling, or some other resolution that focuses on getting the parents to see the harm they are doing.
You can certainly ask that a provision be put in your order of court prohibiting this type of conduct from your ex. Enforcement of such an order is a bit more difficult. You should file a petition for modification of custody. Certainly, at age 14, the Judge will speak with your son and his wishes will be taken into consideration. This interview with the child will likely take place without parents present so your son will hopefully feel free to say what he thinks. Where the child lives will remain an adult's decision; either you and your ex decide or the Judge will.