Dear Thomas,
As someone interested in both physics and music, I found your essay very interesting, and indeed eye-opening. You cover a lot of ground in different areas music theory in just one short paper, and I think this may increase the likelihood that some of your arguments escape notice. I looked at your website, and if I may make a suggestion, it would be helpful to interested persons if
a) you could include some samples that allow the listener to directly compare music according to the tempered scale against the properly tuned one.
b) you could have dedicated web pages for each of the areas in which your framework leads to a better understanding of aspects of music theory.
Finally, it seems to me that among those interested in your work may be
a) music instrument manufacturers
b) musicians, both composers and performers
c) music theorists
d) physicists
e) architects
f) physicians
g) public health officials
h) entrepreneurs and venture capitalists
And each group among this "target audience" has obviously different perspectives, backgrounds, levels of and need for understanding aspects of your work. So, if you have not already done so, you may wish to differentiate your approach towards each group. For example you might consider having sections in your website dedicated to addressing each group separately.
At any rate, your essay was very interesting, and I wish you all the best.
Armin
PS. I noticed that you designed an automatic prescription filling progam. Ha, another commonality, as I am (still) a pharmacist by profession.