Sparks - it's rough, just keep working through it and doing the best you can. I would guess your wife is pissed because she knows she wants more time with son and you may have scooped her, she's mad that she walked away and now sees she maybe had a good thing, she's mad because she doesn't know what to do and you/therapy are just confusing her more, and like you, she's probably thinking, why did it take all this crap for us to start really talking and listening.
My suggestion is maybe less talk, more action and listening. You sound worn out and it's easy to get talked in circles till you don't know what message you are sending. And I think you can tell her that...hey, you're pissed no matter what I say or do, I think I need a break....don't say it that way, but give yourself some distance and space. She needs to figure out which team she's on so you can make some decisions.
Faith is, at one and the same time, absolutely necessary and altogether impossible. --Stanislaw Lem