Try the brand NUBY sp? sippie cups they sell them at walmart and they have almost like a bottle nipple but yet still a sippie lid, they're soft and silcone like a nipple but it's definately a sippie cup. That cup is the easiest to transition over.
With the milk I would switch 1 or the other meaning don't switch over to a cup and whole milk at the same time. Either start the whole milk in her regular bottles she's use to or start formula in sippie cup. I think switching both at the same time might be to much. The easiest way to switch the milk is just add whole milk to the formula and add a little more every few days til it's mostly just whole milk.
As far as when to switch most parents switch at or by age1 but you can wait a bit longer if you want also.