First, the markdown files need to be converted to LibreOffice format with:
$ pandoc {file.markdown} -o {file.odt}
Then from LibreOffice, make sure the Deja Vu font family is used for all the texts and add some air between paragraphs. Font size for normal text is 10pt.
Create the form fields as explained in this tutorial but make sure the font for the form fields is Arial (11pt).
When exporting to PDF, remember to set changes to only "fill in form fields" first.