Find Short Clip of Audio Within Longer Clip Of Audio I need help figuring out a way to automatically synchronize two audio files that are both different recordings of the same source. More info below.



This example is from a concert, where there is only one audio source - the band.




In the first track of the image below, we have three minutes of audio
recorded from the soundboard of the concert venue. This contains a
crystal clear recording of the band's performance.
In the second track of the image below, we have roughly a minute and 
a quarter of audio recorded using an iPhone in the crowd. This audio 
still sounds ok, but is not great by any means. Still, it's very
useable.


Since both of these recordings were taken at roughly the same time of the same performance, the audio in track two synchronizes somewhere with the audio in track 1.







The image below shows where these two snippets of audio synchronize - about the 3 second mark. 





I know that it's pretty easy to synchronize these two audio files up by hand and by ear, but I need to develop a script that synchronizes the two snippets automatically.



The Spectrogram and Spectrogram Log match up pretty well. I'm not sure if I can work with that or not.

Here is the spectrogram comparison:



Along with the spectrogram log comparison:





I've looked into Cross-Correlation of Waveforms using this video, FFT stuff, and other libraries. I'm lost and any help for my college project would be much appreciated!
As good as AUDFPRINT is, I think it is overkill for your problem, as is solving a different problem (where the audio being compared can be arbitrary). You already know what that your shorter file and your longer file capture the same audio scene and you only need to calculate the "offset" between them.

This thread on cross-correlation has a lot of good info:
Cross correlation vs FFT for finding phase between 2 signals

How do I implement cross-correlation to prove two audio files are similar?

If you go the cross-correlation route, I think that phase-correlation (variant) will give you much better results, than simply the basic cross-correlation.

The primary difference is that you normalize your fft coefficients to unit magnitude prior to your inverse-fft, so the phase-correlation is based only on phase information and is insensitive to changes in magnitude/intensity (which makes it more robust, able to synchronize quiet and loud recordings of the same scene)