With Thomas we just switched cold turkey at 1. He was running out of formula so when his formula was finished we just changed to cows milk. We had no problems. We also heated the cows milk as he hated cold milk.
I was not too worried about keeping the bottle, and he had his milk in a bottle until he was about 16 months. When he started decreasing his milk intake, we then started offering it in a sippy.
If Callies is having a small amount of milk in the afternoon, perhaps you could try and offer that in a cup first to get her used to it, and once she is taking her milk well in her sippy cup you can then start switching the other two bottles.