> It may be possible with some hacking and/or extensions to switch Dokuwiki to Markdown but the same amount of effort could also be spent on just writing a new wiki with only the features I need.

I think it's great to write your own wiki, and encourage everyone to do so (I've done it more than once), but it's definitely not easier to do that than to modify Dokuwiki.

1. Dokuwiki syntax is included in Pandoc.

2. There's a plugin (I don't remember the name) that will allow you to not only create Dokuwiki pages in markdown, but let you use Dokuwiki syntax where it goes beyond markdown. My recollection is that it works by using markdown to override common components of the syntaxes while leaving the rest of Dokuwiki syntax unaffected.