L.B.
Um, if you have court ordered custody - wouldn't this be considered kidnapping? Check with your attorney or police department - it may be that Dad has broken the law.
Call today and start the legal process to get your son back.
EDIT: for next year make sure the school knows that your Ex does not have permission to check your child out of school - that way he can't just take him from school.
Good Luck
God Bless