It looks as though the files required to run this have been moved from the link as given to http://michelf.ca/projects/php-markdown/classic/. Took me a while to work that out because I have no idea what I'm doing but when I used the files available in the /classic directory I stopped getting errors that wouldn't let me get to the wiki. I could have done something else wrong, tho, so just leaving a note here. Cheers.
Topic on Extension talk:MarkdownExtraParser/Flow
Thank you for letting us know. I just updated the documentation to point to the classic version of markdown which seems to be the only working one in combination with this extension.