If she already drinks out of a sippy cup, I would just make sure that's what she gets for all meals. Really, I don't think there's a right way or a wrong way to do this, but I think making the switch away from formula to milk is probably the first thing I would tackle. Then, drop the bottles.
For us, we kept an AM and bedtime bottle for DS until he was about 18 months, just because he wouldn't drink milk out of a sippy cup. He still doesn't drink plain milk and has only just now started drinking chocolate milk in the past month or so. So, I say that just in case you find you LO doesn't like plain milk either: I'd go for her getting milk in a bottle vs. no milk at all, ya know?
And I agree, this summer can just go away. Glad you're safe!