Oy, I feel for you.
I bet you'd both benefit from training, e. g. something like puppy kindergarten.
In the meantime, the smell isn't helping matters, on either end. She thinks it means that it's okay to pee. And as for you, well, you need a gas mask.
You may need to clean the place from top to bottom. Use bleach and not ammonia, as ammonia is a component of urine and she might get confused by that.
May I ask where the crate is? Is it in your bedroom, the front hall, somewhere else? Maybe she's afraid at night (I'm clutching at straws here), if she can't see you.