I'm definitely thinking an exercise pen would help a lot. I think she's bouncing around your bed at night because she still has energy because she was crated during the day. Get her some good exercise during the day, whether it's fetch or a good walk and she will more than likely not jump around.
The pooing and peeing in the middle of the night could probably be helped with a pen to if she sleeps in it, she probably will not potty in it.
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