Welcome to flyertalk Paulie.

Good news is that if you dont get to sit upfront from Shannon to Newark, you will get the miles+cash back. Even if you get upgraded on the other flights. However, i wouldnt count on clearing the waitlist early, you might not clear until you are at the gate (has happened to me 2 of 3 times in similar situations). Of course they could clear before, but you never really know.

Bad news, you can only get miles for your butt in the seat. Your wife's cannot be applied to your account. Open an account for her and let her start gaining miles.