Apply broadly and make sure you get into a program. Residency and fellowship are entirely more pertinent to academics than where you went to medical school. Wherever you go make sure you set yourself up for a residency at a university and you will be fine.
Agree.
OP, I am a PhD-to-MD (PhD in pharmaceutical chemistry) and applying for residency this year. There are a few important things you need to do.
First, you were right to retake the MCAT. Most if not all med schools will not accept a score that is over 3 years old.
Second, you need to get some clinical experience. This is as much of a prereq for med school as biology or chemistry is. If you don't have much exposure to physicians and what physicians do, how do you hope to convince an adcom that you've thought out your decision? Even more importantly, how can you even convince yourself? When I was considering med school, I sought out an MD/PhD at my local med school and spent some time shadowing him as well as doing some side research with him. You may want to think about doing the same.
Third, you will want to use your PS to explain the evolution of your career from physiologist to MD/PhD. In my case, I had been doing some clinical research with the MD/PhD, and I talked about wanting to have a more clinical bent to my research as opposed to straight basic science. You can't see patients as a chemistry PhD.
Fourth, you will choose schools by getting yourself a copy of the MSAR (available from the AAMC; just google it), and you will go through the book and cross out every school that is either somewhere you don't want to live, or else doesn't accept residents of NY. Then of the remaining schools, you will want to choose places where your goals fit with their mission. So, if you want to be a physician scientist, don't apply to a bunch of schools whose mission is to provide clinicians to care for the underserved.
I also found the USNWR list of top 50 research schools helpful as suggestions for schools that might be of interest to me. This ranking is largely based upon research dollars for the school, so it will give you an idea of which schools tend to focus more heavily on research. You do not have to go to an Ivy med school in order to have excellent research opportunities while you're in med school, although I agree with you that many state schools may not have the kind of infrastructure you'd be wanting. (Not saying anything specific about NY schools, since I'm from FL). That being said, you want to apply to enough schools to have a good chance of getting enough invites and acceptances, and there aren't enough Ivies to fit this requirement. I agree that 20ish schools would be a good number.
Finally, 29 is young. I was 31 when I started, and many others in this forum are older still.
Hope this helps, and if you have questions, feel free to PM. Also, you should read the FAQs sticky at the top of this forum. There is tons of good info in there, including a sticky I put together of threads that will be of interest for people going from grad school to med school.