The problem I ran into was not with the license for the font, but the format of the font. FOP's TTFReader reported that the MS Gothic font in msgothic.ttc shipped with Windows did not have license restrictions, but rather the version of MS Gothic that I had was in Postscript Type 3 format, which FOP does not supported for embedding in PDF files.
Of course, we could not check in the MS Gothic font, but it could be used by a someone building the docs to produce PDFs if the user has a valid Windows license. In an ideal situation, we would have a compatibly licensed Japanese font in Truetype or Postscript Type 1 format that we could embed into the Japanese PDF with FOP. Tomohito, you are probably the best person to find out if a font like that exists.
I am still investigating the problem with the multiple-page HTML files. It builds fine on the Mac, but I get corruption in the individual HTML pages on Windows. The problem appears to be with Ant's <copy>/<move> tasks. The files that are transformed by the Xerces/Xalan in the DITA transform steps are correct. It is the copy in Ant to add the Apache license header that causes the corruption. I have not determined yet why this happens only on Windows and not also on the Mac.