E.S.
Nuby makes a sippy that has a silicone spout, soft like a nipple. Try giving her milk from a sippy that is transitional like that one, rather than a hard spout one.
I just took my son off his bottle (he was already reduced to 2 a day for a while before we took it away completely) and he doesn't drink nearly as much milk now but he's slowly getting used to it. So be patient. My son only takes a few sips here and there from the cup. It could well take several weeks or even months. In the meantime, he's getting his calcium and protein from other dairy sources so I'm not too concerned about his reduced milk consumption.
It sounds like it's time to consolidate your baby's naps. This also may take some time and require some patience. Darken the room, spend plenty of time winding her down prior to nap and good luck! (I consolidated naps at about 12 months and took him off bottle at 18 months, FYI)