You're doing good, Dan - you have more patience than I think even I would have, and I have a fair amount. (most of the time)
I would like to pass on some advice that was recently given to me (also out of the bible), and tell you to win her over without a word. It's your choice of course, and you know your relationship better than anyone - better than your wife possibly right now too, but I would depend more on the showing her that you love her than telling her that you love her. Have dinner cooked for her on meeting nights; have the house cleaned up. Play with your son and take care of your daughter so she gets a break after meetings, before meetings, etc. Treat her with love and respect. I don't think your words are being received well right now.
As for your son, tell him that you need to speak to Jesus and pray to God on your own for a little while. You're doing some studying, you love them both very much, and they'll let you know what you should do. Tell not to worry, and remind him of how much you love him, his sister (?), and his mom. Maybe make a habit of listening to him say his prayers at night so you're still part of his spiritual life.
Anyway, just some thoughts. You do need to say something to your son, because if you don't, he's going to hear only what they want him to hear, and he's going to be confused and that will make him afraid.
I am keeping you in my prayers also.
Tammy