Is Pandoc being used mostly to join the files? I recently started converting Markdown files to epub (and kepub) for my new Kobo. I load the Markdown straight into Calibre though. On a side note, is there some benefit to mobi over epub? Kepub seems to be the preferred format on Kobo, because for some reason it turns pages _much_ faster than epub and gives access to reader statistics (if one cares about that).
AFAIK Amazon Kindle devices can read mobi files but not epub files (unless you convert them to something else first).
(The mobi format is older, so if you want to read an ebook on your old Palm Pilot PDA then you'll probably want mobi.)