I figured out how to answer this, but I went out of the frying pan into the fire.
I can get to a file in the .esb by calling getClass().getResource("path"), being sure to start the path with a "/" to indicate it is from the root esbcontent directory.
So I managed to load the XSLT file, but it also references an external file as an XSD. Once again, using a simple relative path inside the XSLT is not working. I tried setting the SystemID on the transformer (useful advice from http://stackoverflow.com/questions/7236291/saxon-error-with-xslt-import-statement), but that didn't help. I suppose I need a URIResolver, but I don't know how to resolve the path since it isn't part of the regular filesystem.