How old is she? Poor little pumpkin, sounds like she had a pretty big surgery! Can you just use the bigger crate with the bed on one side and the pad on the other? Since she is a puppy it is harder for her to hold her pee, it is also not healthy for her to have to.
Yes- you can get up a couple minutes before 5:30, take her to her pad and make her go poo. You might have to do that a couple times so she knows she is to go poo on the pad.
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