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First, I don't think footnotes translate easily to HTML. Endnotes are way easier and more appropriate.

The problem here is that HTML isn't semantically rich enough to do these things automatically. You need to manually do the numbering.

I use docbook XML to create citations and endnotes. Very easy to do. Then I use docbook XSLT to output everything in clean HTML. That is a powerful solution, especially if you are comfortable using XSLT. www.sagehill.net/docbookxsl/Footnotes.html
Another out of the box solution is to edit source in Markdown language and then convert everything to HTML. I see that Pandoc has a footnote solution rmarkdown.rstudio.com/authoring_pandoc_markdown.html#footnotes
It would be worth looking into what capabilities Adobe Indesign has for creating footnotes/endnotes. They have an Export-to-epub capability, and maybe the output renders the footnotes/endnotes in a nonsucky way.

Failing that, regular expressions are the way to go. But you might look into this: www.w3.org/TR/html5/common-idioms.html#footnotes
At the risk of trying to simplify your need, a lot can be said for just doing it manually rather than trying to change your production process. This is true especially if you already know the number for each footnote -- like, are you just reproducing the footnote number from a public domain work? Maintaining under 100 citations manually might be less trouble than you think.


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