Glad you had such a great experience at UMass! It really is an excellent school and I hope you keep us in consideration as you make your choice!
It's really hard to say where to go - you are going to get an excellent medical education at any US medical school you attend - it's really a question of what is right for you!
Which program did you like the best? What school do you think had a curriculum that would best fit what you know about your learning style (are you even planning to go to class)? Which school had a 'culture' that felt like you would fit in? Which school has the most opportunities to help you on your way to your goal? Is money an important factor for you?
How confident are you that you want to go into neurosurgery?
The first few questions I suspect will be easier to answer than the last (3rd year can be a magic time where you find that you love something you never would have imagined doing!), unless of course you have a lot of past experience with neurosurgery that has you pretty confident that that's your calling.
What I can say about UMass is this: We have a great community feel, very collaborative learning environment, and a great new facility with lots of up-and-coming research. I agree with you that that #46 research ranking is going to rise very quickly! But I can also say this: We're the med school of the Commonwealth and we're very big on primary care (top 10 for that!). It's not to say that my classmates don't go into specialties (more and more do every year), but rather that more of your colleagues here would be interested in primary care than at other schools.
So what does that mean exactly? I don't really know. I suspect that it would be quite easy to get involved with research here, which it sounds like you are interested in, and I can tell you that the faculty here are very welcoming and supportive of students in general, which would make for excellent mentoring!
On the other hand, even as someone who LOVES UMass, I might suspect that Harvard might be the better option for neurosurgery (again if that's what you are confident that you want). I think that having the Harvard name, and maybe more importantly, having experience with and letters of rec from Harvard neurosurgery faculty, could be helpful in trying to match in such a competitive field. Like you said, if you have the drive and the passion, you're going to make it happen wherever you go, but you might have the slightest edge coming from Harvard versus UMass. And if you do end up in Neurosurgery, you are not going to have any trouble paying off the extra 100K in loans, you know? (Sorry, don't know much about Emory's programs, didn't apply there!)
So you've got to weigh your options out! That's just my advice (only an MS II, so grain of salt!). I turned town WashU for UMass and I'm super happy where I am now with no regrets. It was the right choice for me!
But the nice thing is that this is the best kind of hard decision to have to make! Best of luck to you!