There are several methods available for improving our ability to identify guitar notes. For example, each note has a unique harmonic signature. Presently, we only take the strongest harmonic. However, if we look at several harmonics, we could take advantage of individual note harmonic signatures.
Journal of Object Technology
Lyon, Douglas A., "The Discrete Fourier Transform, Part 5: Spectrogram" (2010). Engineering Faculty Publications. 72.
Douglas Lyon, “The Discrete Fourier Transform, Part 5: Spectrogram”, Journal of Object Technology, Volume 9, no. 1 (January 2010), pp. 15-24