Nothing fancy because I had to avoid destroying inline code which can have wiki syntax (e.g. windsor config has "{{...}}"). There was also all sorts of random escaped wikitext that people needed to get STW to display what we wanted. Along with the conversation I skim read the majority of pages as I went and rearranged things, fixed headers that had the wrong indentation level and many other problems.
If you've got a cleaner set you might be able to find some tools but I didn't find anything I was confident to run. I basically had a script using grep (with --color) that would display all in wikitext symbols (i.e. [[, [[, {{, }}, @@, '', ''', <, >, and those annoying quotes from Word). If it looked good I used another script to replace a few of those symbols. I then jumped into Atom and manually edited headers and a bunch of other things, then ran the first script which also ran markdownlint (
https://github.com/mivok/markdownlint) until I had no more symbols left and no more lint warnings, I then finished by having a look at the markdown preview in Atom.
Yep, sounds pretty painful, but I did a lot of clean up as I went and deleted a bunch of duplicate content, merged some pages, cleaned up some code samples, etc. I did most of it while watching TV as to burn the least amount of real time doing it.
Sorry that I don't have a silver bullet to offer.