I agree with niknak - relax and it will work itself out. It's a big change right now and your little one is working herself into it slowly. My daughter sounds like she's right on target with your daughter for height and weight at one year - she's now 16 months old. She wouldn't touch milk at first and I ended up having to put strawberry powder flavoring in it (a small amount) to get her to drink it (like niknak, my pediatrician said it was totally fine to do). My daughter drinks approx. 7 or 8 oz in the morning when she wakes up (basically, one tall sippy cup full) and then again at bedtime. Other than that, she gets other dairy products such as cheese, vanilla pudding made with milk, etc. throughout the day. The only other drink she has all day long is water - she consumes tons -- it sounds like you do this as well. Don't worry about confusing her with the bottle and cup - transitioning slowly works for some kids. It's a big change to milk and away from the bottle at once. Since I used the strawberry flavoring, I switched immediately to the sippy cup, but my daughter was mainly using one at that point so she didn't mind. I'd definitely try giving her the sippy cup as often as possible, but don't sweat it - she's still very young.
As for food - my daughter gets her milk in the morning while I prepare her breakfast and then gets a snack when she wakes up from her morning nap (if she takes one). Her lunch use to be a good healthy meal, but she has become picky lately so I've resorted to some sliced cheese, crackers and fruit. For dinner I am giving her cut up chicken, pasta, rice, mashed potatoes - depending on what she will eat that night I give her one or two of the above and then some more fruit or two Gerber cookies after her meal. She snacks a lot more during the day lately - if we are out she's looking for breadsticks, etc. to munch on.
Hope some of this has helped. Definitely just go with it - it's one thing Iv'e learned, ALL kids are different so go with your gut. Good luck.