Your W just seems bazaar (IMHO), when reading how she couples her and D together as she makes accusations against you. Instead of accusing you of treating her in some manner (the way most unhappy W's do), she always seems to say D and her. Can you see it? Yes, the child is the center of your lives, but your W's statements have a strange tone.
Exactly how are the two of you are separated? You live together, eat together, sleep in bed together,o and still do family events together. She announced to you that you're separated, so she can continue to have her A while benefiting from the M. Has this "separation" taken one thing away from her?
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W went to bed at 4am again. It's dawning on me that maybe I need to let her know that custody will not be what she thinks it will be
No! Custody is for her to find out and deal with it. If I were you, I would be concerned that she is going to present false information, to sway custody in her favor. She has made the choice to exclude you from her life (and is trying hard to exclude you from daughter's life, too)........let her experience the fallout of her decisions.
It is not about what you feel should work in your M. It is about doing the work that gets the right results. Do what works!