Poor Penny Hopefully with the Innova her levels will improve. As a stray, I'm sure she wasn't getting near all the nutrition required. As for the housebreaking...have you tried keeping her confined to a limited area, like gating off the kitchen? I've only had to housebreak one dog in my life. Taking her out frequently, praise and reward when she went outdoors, picking up her water bowl at night, and a lot of patience, did the trick for us. I'm not sure how you're using the pads, but I 've found that using them can mistakingly teach them to GO on the pad. Hopefully with time and a lot of encouragement and positive re-enforcement, she will learn not to fear the crate. Have you tried feeding her in there with the door open, putting her toys in there? Making it a fun and happy place to go into was the key to getting my Star to enjoy going in there.

Poor girl is probably still a little confused and adjusting to her new home. I'm sure with time and a little patience, she'll get the hang of it. She's such an adorable girl! Good luck and hugs to beautiful Penny Lane!