@uvok I can totally relate to the issue with Markdown, Jekyll, and Gemini. I also have a blog built with Jekyll, but I have no idea how to convert it to Gemtext. Furthermore, some Markdown files also contain HTML, such as MathML.
@mark22k you might be able to use
https://git.uvok.de/html2gemini/
To a degree. MathML probably won't work, though ^^
html2gemini - HTML2Gemini converter