First of all congrats on all the great options!
As a fellow MD/PhD applicant, I feel you on your current dilemma of location vs. research. If you want to end up in the Midwest, do you want to go somewhere else first before going to the Midwest, or do you love it enough there that you want to do MD/PhD training and residency/etc there too?
Anecdotally, students tell me that 3-4-1 is slightly better in their eyes, but to faculty and in the long run of a career, the specific curriculum structure doesn't matter it seems. Even if you do a PhD in an area that isn't directly tied to whatever specialty you go to match in, it'll make you super interesting and qualified to residencies. I personally think I would prefer something like 3-4-1, but it's not a major consideration for me.
I've heard that as long as it's an MSTP, prestige doesn't really matter?
I can only really speak to UNC (disclaimer, accepted to UNC), but I do know their history of getting F30s is good and their public health school is amazing. I didn't think I would like Triangle area but it's actually really nice here! I'm biased, but I think it merits visiting in person if you can.