Markdown parsing works OK now
After getting it working somewhat, I realised that my pre-parsing fix (manually replacing triple backticks with HTML code tags) allows me to use markdown.pl without issues, which is nice, cos it formats the code well, with no need to escape backslashes to preserve formatting.
So, I have made markdown.pl the default parser, but left some code in create_page which can use other stuff too - markdown.sh and md2html.sh.
The md2html.sh script uses the GitHub API, but you might hit rate limits or not have a network connection, and it has issues with formatting newlines in code blocks, so it's not the default parser.