The books Tuning, Timbre, Spectrum, Scale [1] and Rhythm and Transforms [2] by Sethares have a lot of detail about the perception of higher level phenomena like pitch and rhythm. Plus he's an electrical engineer, so you get some code out of the deal. He doesn't dwell too much on the neuroscience aspect though--in both cases he's after a more functional explanation.

[1] https://sethares.engr.wisc.edu/ttss.html [2] https://sethares.engr.wisc.edu/RT.html