I've decided to scrap the eXist rebuild for a few reasons:

The XML schema was not meant as a final destination for the data. SA created it as an ad hoc intermediary step between SD's raw data and the MySQL database. So, the schema doesn't lend itself well to being the backbone of an eXist architecture, particularly when it comes to searching and generating human-readable values. The structure of the data is highly relational and is a good fit for SQL, which, of course, was SA's original intention.

That said, my original motivation for the eXist rebuild still stands. The current method of translating the XML to SQL involves using XSLT transformations to generate SQL statements. However, every time the schema is updated with new structure or values - which is happening a lot - the XSLT stylesheets need to be updated as well. So, to get around these difficulties, I'm going to write a PHP script that will convert the XML to MySQL, likely use SimpleXML. It won't be the fastest script I've ever written, but since it will be a one-use-per-dataset kind of thing, speed isn't a big issue.