I hope everything works out with Penny's protein levels. I'm sure you can straighten her diet out--who knows what she had been eating
As for the housebreaking, it sounds like things are getting better--especially if she crawled in the crate herself!!! Riley was deathly terrified of his crate, so I penned him up with Abbey--he still barks a little, but nowhere near the mess he was when he was in the crate.