I have never agreed with the physical stuff. I think it destroys trust and can go south quickly. You want a puppy that minds you and trusts you. As well as you have done with the other training, I think you can stop the nipping, which is pretty common with puppies, especially, teething puppies, by just being consistent with whatever method you use. Have you ever tried using pennies in a can when she does this? I am only suggesting trying that if a big, loud no doesn't stop her along with placing her in an x-pen and ignoring her for awhile. Just be consistent and I think she'll associate one consistent correction with that behavior. I believe she is teething and that is making the problem worse. Does she have any bully sticks to chew on? You are going to have to use a deep, authoritative voice to get her to pay attention. If she senses any doubt or fear in your voice, then you will never get her trained. I hope things get better, but like I said, she's only 12 weeks, so you are going to need to be patient and consistent with her. You took the place of her mommy.