Other then some missed opportunities to validate I don’t think you did that bad. There is absolutely nothing wrong with standing your ground. I’m glad you told her you want 50/50 custody. When decisions are based on emotions there are sure to be consequences.
Try very hard to not become obsessed with her comment that YOU clearly don’t want to work on the marriage. She’s projecting. You’re kinda in a tough spot because right now it seems remaining separated Is her best option right now and that is going to mean you remain in limbo.