She is doing very well with the peeing for such a small pup. I do think it will take more time for her to control her body when it comes to pooping. My Teddy had a sense of urgency up to a year, but he has access to a pad at all times. Max had control much earlier.
The only thing I can think of to suggest is to keep her out of her crate longer early in the morning and near her pad. I remember puppy days waking up at 5 am and losing sleep.