Sarah,
When I weaned DD onto cow's milk I did mix it with formula - I did one week two thirds formula, one third cow's milk, next week half and half and the following week two thirds cow's milk and one third formula - that seemed to work fine with her.
Are they refusing the sippy cup at bedtime because they are tired and associate bottle with bed? It took a while for my DD to want to drink milk from a beaker, probably because of that. I would continue using the sippy cup for lunchtime and maybe continue with the bottle at bedtime for now, while they are getting used to the changeover.. (that's just my opinion).
In terms of quantity, again, I think 14 oz is fine, together with the cheese and yoghurt. I think (and someone will tell me if I'm wrong) that they should be getting about a pint of milk a day, but that DOES include cheese, yoghurt etc.
HTH!