I have just recently decided to start using Engage NY because my school does not have any Common Core aligned materials. Here was my initial thought. As for fitting in Math Daily 3....I think that in a perfect world, one of those Engage NY lessons will only take 1 day. I think in reality they will take part of a second as well. So, I was planning on teaching a lesson and then the 2 days following the completion, have the math block be just Daily 3 (with little mini lessons of course) so I can pull small groups of students who did not get the concept or eventually groups to enrich. After those days, I will start the cycle over with a new concept. I guess it is a modified form of Math Daily 3, as it is not actually a DAILY occurrence, but I think it is as close as I can get.
Also for differentiation, so you have the groups a few times a week, that is definitely differentiation, and then with those practice sets I would modify them based on IEP needs like less questions, answering in a small group setting or working with a partner.
Hope that helps!