I've got another idea!
I like your plugin better for several reasons. One of them is that your plugin uses footnotes in a separate file, not inline. I need that.
What I think I will try is using your test.epub and adding the bodytext and note page html's that I want footnoted and deleting your little test files, and updating with the correct css for the footnotes. Then, run your plugin and save the two files externally. Then re-import them into the main epub I'm working on. I should have time to try this out by tomorrow.
I would totally be willing to do this, if it will let me continue using your plugin..
Update: Ok, I've tried it on a couple of files that were already footnoted, and it functioned perfectly!