About the final accuracy of an FFT applied to note recording sample files, it's 
like
if you have a number of waves in you FFT interval, they seldom will wrap around 
at sample
boundaries, and certainly if you want an accurate match in your FFT, the FFT 
interval
should as closely as possible match the wavelength of the lowest frequency in 
you tone.

So you'd have to find out the number of samples per wave, and use a multiple 
number of
waves from your sampled file until the number of waves (in terms of as accurate 
as
possible matched sampled in floating point) becomes close to an integer number.

Then adjust the bin size, and hope transients (there's all kinds of electronic 
coupling
going on) and disturbances (which do not necessarily fit in the same harmonic 
analysis
interval for repeating waves) aren't too much a problem.

T.V.
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