<p>Your idea about perhaps transferring after the MA is a very reasonable one; many of the “top” schools, including Columbia, frequently accept transfer students at that level (for one thing, they save money on the fellowships, because the program takes a year less, but also there are many highly qualified students who apply at that point – and they have proven themselves by their academic success and by participating in conferences, etc.); do take a look at Stony Brook, if that is not too far away. (An example of someone who did that is one of the new professors at Rutgers – who, according to the website, went to Stony Brook and then Columbia). Theory is very different from music history – some programs don’t even offer that as an option (e.g., UC Berkeley), while others have strong theory departments that include history of theory (kind of a meta-subject) – e.g., University of Chicago.</p>