Finally! A paper for self-similarity matrix comparison in the Music Information Retrieval literature -- doing what I want it to do!

Measuring Structural Similarity in Music - Juan P. Bello

I can definitely use this to compare music to movement.... It must be sensitive to small variations since he is using it to compare different performances of the same piece of music. He is using it for tonal music, but I can just use MFCCs (& maybe amplitude or STSMPS?) instead of the chroma-based features and CENs he's using, since (except for the Giselle null comparison example, the music is not necessarily pitch-based that I am analyzing) But anyways, that won't matter. I just need the comparison methods.

He is also using Recurrence Plots instead of self-similarity matrices, but they are similar measures. He then uses the Normalized Comparison Difference (NCD) -- something that is common to use in bioinformatics for genetics comparison -- to come up with a similarity score between the recurrence plots. Then, it looks like he finds threshold values for pairwise similarity and then uses the measure to retrieve performances of the same work of music. The measure is not tolerant of global structure changes (eg, if someone repeats a section and another does not) but that actually doesn't even matter for my application.

Tools that he uses:

Toolbox for Recurrence plots:
http://tocsy.pik-potsdam.de/CRPtoolbox/

Normalized Compression Distance:
http://www.complearn.org/ncd.html

I also had this idea in the shower that perhaps I could define the relationship between the structure of dance and music by their distance matrices. So if I had enough data, I could do ANOTHER NCD on the NCD data and see if the different performances of Variations V music and movement relationship (ie, the distance matrix between their similarity measures  (whether RP or SSM) ) cluster together -- as opposed to other interactive and non-interactive dance.

I found this link which provides a lot of good information about music information retrieval -- mostly because I accessed the textbook for the course through my university's library (he had a lot of papers on structural analysis of audio via SSM so I just looked up his name). I thought about using the method described in the textbook for the segmentation of self-similarity matrices to determine what the actual repetitive structure is but I think that Bello's approach is more apropo to my musical analysis problem. I would definitely apply the segmentation / path method as well if I had time... but man, do I need this paper to be over.