First, get your attorney. Second, is the agreement in writing? If so, then you should have the children unless something terrible happens and you can't take care of them. Third, have activities planned with your children so it's impossible for her to pick them up.
And finally, show your ex-wife your concerns about how the the imperfect men inside the WTS who hide pedophiles who are also imperfect men, the incidents that have occurred. In particular, I am thinking about the many pedophiles that attached themselves to single, JW women because of the children. I am also thinking of the many JWs who molested kids during "rides" when their parents were not there. Show her newspaper and court reports. Silentlambs and watchtowerdocuments. will make it quicker research for you. Don't bash her religion, but just set it very clear that you have legitimate concerns about the children being with any other JW, but her.