Thanks. The first one is worked around, but the perl script which generates the HTML output should be modified to also generate (not just copy) compare.html and to allow specifying the main HTML output file name. I used index.html there but it defaults to "glest_autodocument_summary.html" (which does not work as a directory index overlay).
I don't intend to fix the second issue at this time, it's a result of applying the main websites' imperfect CSS to the HTML output generated by the convert_faction_xml2html script.