I was able to backup Mongol using AnyHD DVD. I used tsmuxer to demux the raw H264 file, AC3 file, and subtitle.sub file. I used MKV merge to make it into an .MKV the only problem is that MKV merge doesn't pick up the .sub file. So now I have an .mkv file with no subtitles. Is there a way to make an .mkv file to include the .sub subtitles file? Again, I have all the raw files demuxed and I also have the files in BD structure as well.
Convert the subtitle to a format that mkvmerge will open, .srt for example: http://www.robelix.com/sub2srt/