Hi Miriam,
MEI does indeed support shape-note notation.
It also allows the comparison of image regions without encoding the entire group of songs. In the following example --
<facsimile>
<surface>
<graphic xml:id="g1" xlink:href="A_1.jpg"/>
<zone xml:id="g1z175" ulx="120" uly="992" lrx="450" lry="290"/>
</surface>
<surface>
<graphic xml:id="g1" xlink:href="A_2.jpg"/>
<zone xml:id="g1z175" ulx="120" uly="992" lrx="450" lry="290"/>
</surface>
</facsimile>
surface elements are used for each page, graphic elements declare the image associated with the page, and zone elements define the regions of interest of the image. The attributes ulx, uly, lrx, and lry (upper-left-x, upper-left-y, lower-right-x, and lower-right-y, respectively) capture the image region's coordinates using the coordinate system of the image, similar to the way image maps are done. The @decls attribute is available on facsimile, surface, and graphic elements in order to associate these elements with metadata in the file header.
I don't believe this will work for PDFs so you'd have to convert them to some raster format.
However, having done this, features encoded in the markup (measures, notes, etc.) can be associated with one or more zones using the @facs attribute.
<measure xml:id="m2" n="2" facs="g1z175 someOtherRegion"/>
If the differences are all at the measure level, then this markup may be all you need. This provides enough information to locate, in this case, measure 2 in all the appropriate images and navigate between the various images and regions.
If you are interested in providing commentary about the markup features, then use the annot (annotation) element, like so --
<annot plist="m2">Measure 2 is really cool!</annot>
The @plist attribute contains the ID of the feature you want to comment on.
This is just a basic introduction. If you'd like more info, feel free to write to me at info (AT) music-encoding (DOT) org.
Good luck with your project!