Three things helped us with our oldest and are helping us with our second, too! They are extra time, a sense of humor, and choices. Let me explain.
I build in extra time to everything because I know it's going to take longer than it used to! Bathtimes are almost an hour now. Getting dressed takes about 15 minutes. Making lunch (they HAVE to help!) takes about 30-40 minutes. I just start much earlier than I want to or really need to so that our home runs more smoothly. (Oh, yeah... add getting into carseats on that list, too. There are more "rules" every day... who pushes the buttons, which foot goes into the minivan first, etc.)
A sense of humor is a must. As much as you can, let her do the things that she wants to do. She will amaze you with what she's picked up! On the other hand, she is still learning, and some of the ways she tries to do things will crack you up... if you're not looking for a reason to get angry with her. My oldest son wanted milk, so he opened the refrigerator door, stood on the bottom of the fridge, grabbed a full gallon of milk, pulled it out, dropped it on the floor, and dragged it over to where I was changing his little brother's diaper. Basically, he dumped a gallon of milk on the floor! What else could I have done except compliment him on his go-get-em attitude, have him help me clean it up, and give him water instead? It really was hilarious, after I took several steps back in my mind!
The third thing is choices. Yes, your daughter is asserting her independence. It's scary for her to think that she has different ideas than you, and it's scary all the choices she has out there! I would choose two (or maybe three) things and let our boys make their choices. I had already narrowed things down to a few manageable options. Whatever they chose, I was okay with it. But they still had the freedom to decide what they wanted to eat, wear, etc. For naptime, I would give them a choice between two or three books (they could choose one), two blankets, two toys/stuffed animals (if your daughter sleeps with them), etc. That way, my boys made naptime their own, and if they weren't happy, it wasn't my fault. I would say, "You chose the red blanket. You can have the green blanket tomorrow, if you still want it then."
This too will pass. Good luck!