Surprisingly I have not found mentioned one of the greatest research tools for investigating temperaments:
TempEst: http://www.isophonics.net/sawa/tempest/
Just upload an .mp3 or .wav file with a recorded solo piece played on a harpsichord with no other instruments, (YES harpsichord ONLY, NOT PIANO) 
I am still trying to figure out how it works, according to this research paper, in its development they used the modeled Harpsichords from Pianoteq
Quote:
The real harpsichord recordings were played by Dan Tidhar on a Rubio double-manual harpsichord in a small hall. The synthesized recordings were performed on a digital keyboard by Dan Tidhar and rendered from MIDI files using the physical modeling synthesis software Pianoteq (Pianoteq, 2010).
The version used was Pianoteq 3 see the acknowledgements section of Estimation of harpsichord inharmonicity and temperament from musical recordings 

Trying out TempEst the Online tool for estimating instrument tuning parameters
But when trying to identify temperaments, even though the results of TempEst are very accurate and I believe this online software to be the key to study temperaments, I still cannot get this online software to identify equal temperament from a .wav or .mp3 file of a midi rendered by Pianoteq, either playing the built-in Equal temperament, or the neidhardt4.scl Equal Temperament scala file. 
Surely if they had 100% success (read it here) identifying the temperament of the midis rendered by Pianoteq Version 3. My 4.5.5 version of Pianoteq should be as accurate. 

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