Training a recently adopted 2 yr old JRT

I have two questions. I had recently adopted a 2 year old JRT from the Human Society. Unfortunately, Maggie was kept in an outside kennel all year around, 24 hours a day. She was never taught even the most basic manners.

My first question is where should I start on teaching her general training? She is somewhat housetrained, but has her "accidents". She seems, on the majority, not to respond to simple command 'come here', but then again at times she will respond, which leaves me confused as to if she understands or not. When I call her name, she will occasionally look at me, then ignore me and continue walking/running the other way. When I say NO, she will hesitate and then proceed to do what she wants.

My second question is, over the month that we have had her she has become more aggressive and defiant. I don't know if it is dominance or she is beginning to feel more comfortable in her new home and is now beginning to test me.

Your advice would be most helpful.