To the point: I'm hoping to find a topic that combines "computer music" with mathematics, or maybe more correctly; a mathematical topic on a fitting level, that has (some) relations to computer music (in a broad sense).
If you're interested in synthesis/DSP, I recommend to study operator theory and numerical analysis. All of your transforms come from analyzing differential/integral operators, their eigenfunctions/values, and inverses.
Music theory itself is pretty mathematical, but it's practically a pointless endeavor to try to apply mathematics to "explain" music. You just wind up finding structures (like the lattices with minor and major thirds along the axes) with practically no relevance to the real experience of music. However, I believe that studying dynamic systems (non-linear operator theory) has some promise for physiologically based theories of music. I've been thinking about doing a math masters as well....and those are the two topics that I consider most significant.
Chuck