Welcome!
Naomi is very cute. She looks like she may be a French lop – at least in part.
As for your issues:
You’ll want to start her out with a much smaller enclosure of some kind rather than allowing her to free roam. What she’s doing is marking her territory – or at least trying to mark what she thinks is her territory.
Having said that, her current cage is too small. To solve both of these problems, I recommend getting an x-pen at least 36″ high, to allow her a contained area with enough room for exercise. When she has a small area that she can claim as her own, then she will be less inclined to do her business all over the house. To start litter training her, put a litterbox filled with rabbit-safe litter (eg. CareFresh, Yesterday’s News) and some hay into a corner – she may pick a corner that she likes best.
It would also be a good idea to find out for sure if she was spayed, or at least try to. Calling the humane society where she was previously or asking her previous owner just to know 100% is a good idea.
As for the ankle biting, the best thing you can do for right now is to make sure to wear something that covers your feet and ankles when you’re around her, and/or you can use bunny language to tell her you don’t like it. When she nips you, squeal loudly to let her know it hurts. You can also sit up and turn around away from her. This is bunny language for disapproval.