SOT, I see what you are saying. Your son is not feeling success in any sphere of his life right now. And that is not good.
I commend you for stepping up. I think it would be great if you could get your wife more interested in her son's education. Some Witness parents are more inclined in this direction because it makes their religion look good when the kids are successful in school. It "gives a good witness." Maybe you could appeal to that sentiment? If you can in any way construe something as being a "good witness," JWs will often come aboard.
If you could find something to do with the boy that will help him feel successful, that would be great. He needs the self-esteem boost right now. Can he work on the cars with you? Or around the house? Or on some computer programming? Something to make him feel competent.
Never underestimate even just shooting hoops with him. It will help him bond with you and let him know that you are in his corner no matter what. That is the factor that really makes the difference in how kids turn out. His life is stressful. Be his rock.
Best of luck,
GreatTeacher