I don't have any good web links, but a couple of books that I've found useful are The Science of Musical Sound by John R. Pierce and Harmonic Experience by W. Mathieu. (The former is more focused on sound and scientific theory, whereas the latter is more focused on understanding music in a way that would be useful to a musician or composer.)
On the Sensation of Tone by Helmholtz is also worth checking out if you want to understand where a lot of the modern understanding of just intonation comes from.
The thing I don't quite understand is why many seem to argue that major chords aren't inherently more "consonant" than minor chords, and that it's just psychological/cultural, despite the mathematical consonance that seems to be inherent of major triads.
"Consonant" vs "dissonant" is subjective: it's a matter of perception, taste. The way you test the hypothesis "This chord is more consonant/more pleasant than that other chord" is by asking a lot of people. Just like "steak tastes better medium-rare than well-done". Physics & chemistry can inform the discussion but it cannot prove or refute the hypothesis.
