Fair enough, thanks for the work you're putting in on this. Would it be possible for me to look at the source code? I understand if you don't want me to be able to change anything, but I'd be curious to take a look and see what you're doing so far, to see if I can figure out how to make it work with notes.
EDIT: talked to my friend who's more educated in frequencies than I am, and the ones being shown don't match up with what they "ought" to be. Theoretically using the peak should work fine, but the peak isn't matching what is expected (i.e. A4=440Hz), even using sample tones.
I did some testing and I think the problem may be as simple as some bad math - I tested pure tones and the spectrum looked reasonable, but the Hz number itself was off. Here are all the Hz I tested - what was played on the left, and what was heard by AAI on the right:
100 = 48.16
150 = 61.17
200 = 71.23
250 - 80.27
300 = 86.37
350 = 91.52
400 = 97.03
450 = 100.78
500 = 104.30
550 = 107.46
600 = 111.09
650 = 113.67
700 = 116.13
750 = 118.36
800 = 121.05
I notice two things - first that the "heard" number is always lower, and that it keeps getting further and further off. 50Hz played difference at low frequencies makes a 13Hz heard difference, but at the top end it's only a 3Hz heard difference. So I'm thinking there must be some math error with how you're converting frequencies to a Hz number? If the number is right then it should be easy to convert to a note just using the A4=440 table.