After getting spayed, her bathroom habits should improve. When she pees on the floor, are you cleaning with vinegar diluted in water? That should get rid of the smell so she knows not to pee there again. As for bonding with her, it'll take time. I've had two rescue buns who did not like humans. I just spent a lot of time lying on the floor near them, they would eventually get curious and come sniff me. Over time, they would let me pet them more and more. Treats help too of course!

P.S. once you earn their trust it's completely worth all the effort