Change that if you can. What she wants more than anything right now is "not you". Once a woman steps over the line into WAS land, things in her head have changed drastically. She isn't happy, she's not exactly sure why, but she has convinced yourself a lot (or all) of it is because of you and if only she can get you out of her life things will get much better. So the best you can do for her right now is as the others said above, pull back and give her time and space. Eventually she'll realize you're not the problem after all, but it will take time.
Please understand this is a marathon. She's not going to change her mind about the M anytime soon, it's going to be many months or (more likely) a year or more. Things will probably get worse before they get better as her father will no doubt pass away while you are separated, and that will just cause her to go farther down the rabbit hole.
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She recently said she doesn't know who she is. She doesn't think she's right for me.
Oh she thinks she knows. She thinks she wants to be a swinging single and get her groove on. She's just telling you this stuff to try and placate you or "soften the blow".
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She was sexually assaulted in high school and never talked to a therapist. May be some post-partum and possibly depression now. She knows she needs to talk to someone but is scared to start the conversation for fear of breaking down completely (her words). She said she wants to see if the separation helps her to realize what she may be missing.
Don't talk to her about this or the R at all. Your convos should be limited to your son and the weather. If she wants to see a therapist she will, but don't try and push her to do that because it'll be yet another excuse to blame you for how she feels.
Leave her alone, read DR, read Sandi's rules every day, lovingly detach. Work on you. Focus on your S. Get out and GAL. Get in touch with old friends and make new ones. Read relationship books but don't tell her you are.