There was actually some confusion about this. But it seems like in Cornell's curriculum, you can take Step 1 anything during the MCY (so you can do it right after finishing the pre-clinical stuff or after finishing all of your clerkships, though that would coincide with Thanksgiving and Christmas, with about 7 weeks for studying). So you'll be done with everything by December of the major clinical year. This is a little bit different from other schools with a condensed preclinical curriculum as they tend to take January and February off right after the MCY to study for Step 1. In the old/current curriculum, the MCY used to actually be 59 weeks total (excluding Step 1 prep). In order to make room for the 7 weeks needed to complete the MCY in one year, they're cutting down some of the clerkship time, which despite what that means, won't affect your clinical experience at all compared to other schools. For example, currently, Cornell's medicine and surgery clerkships are 12 weeks, which are much longer than what other schools tend to have (they normally fall between 6-10 weeks at other schools, with 8 being the norm).
And yes, there is time dedicated for research... There will be 6 months of protected time for research (and up to 9 if you need it).