Okay... we went through a similar situation.
We were down to a bottle in the morning, and before bed. She wouldn't drink milk from a sippy at all, just water- loves h2o. I did the gradual transition to milk from formula too, never actually mixed milk and formula, just did one bottle at a time. We started offering afternoon milk in a Nuby, the sippy cups with latex spouts. Then a few weeks later, her morning bottle in a Nuby, with a bottle back-up. The first few days, she drank first from Nuby, then from the bottle, on about the 5th day, she just drank from the Nuby. About a month after that, we started the bedtime bottle in the Nuby with a cheese snack.
SOOO, it took about 2 months to make a firm transition from formula to milk in a sippy. She will now drink a few ounces of milk from a regular sippy at lunch, and after dinner. But for the most part, milk still comes from a Nuby.
I'd just take it slow... she'll make the transition, but it may take time. I keep dd's milk close by and offer it frequently, but honestly, she would rather have water.
Good luck,
Trish