Yes, the MP3 file has fundamental frequencies - all other frequencies you hear are caused by bad electronics in the sound-generating system (producing overtones because of lack of fidelity) and noise generated by the recording equipment.

But you don't need to be too detailed when scanning the sound.

Id doesn't matter if you are 10Hz off when measuring the frequencies - you can anyway translate to the standard frequencies from the note system.

In the same way, the original system was most probably too stupid to vary the tempo of the sound, so every tone should start and end on x*n and y*n where n is the base tempo.

If you have a friend with good ear, he should be able to just listen to the sound and enter it by ear on a midi keyboard.

And as I mentioned, you can quite easily download a bit of FFT code from the net and feed the audio in sections. Ignore everything but the fundamental tone and the time when the fundamental tone changed frequency. I would guess that a couple of hours would be enough to have something able to produce a file like:

0:0:0,000 970
0:0:0,010 973
0:0:0,020 970
0:0:0,030 978
0:0:0,040 969
0:0:0,050 742
...

If you play the file in WinAmp and look at the graphic equalizer you can clearly see the frequency - with FFT you could get a spectrum analyzer with 1024 frequencies in which case you will clearly see both a number of bars representing the fundamental frequency and then overtones.

Using a tiny FFT program, you could quickly process hours of audio data.

But if that was all audio you need to care about, I would look for a musician friend and have him play it by ear.