[Perkin]

Right, I've done it with the small example given.
It's three Search and replaces, Two on the orig markdown text file, then when converted to epub, a S&R done in Sigil

Also, the footnotes have to be seperated by blank lines, instead of on following lines as in example.

Open the original markdown txt file
Search

^\[(\d+)\](\S+)

Replace

<sup>\1</sup><a id="fn\1" href="#fnr\1">\2<a>

Edit: replacing all occurences

Then
Search

(\S+)\[(\d+)\]

Replace

\1<sup><a id="#fnr\2" href="#fn\2">\2</a></sup>

Edit: replacing all occurences

Save file, convert with calibre to epub, Using pagebreak in structure detection with default Xpath expression, so each story would the be in their own file.

Then open in Sigil,
Search

../Text/index_split_000.html

Replace with nothing.

Edit: replacing all occurences in CodeView, and replace in all files


Save, you should then have the correctly done file.