Examining the text in your example that needs to be turned into a footnote I assume that all such text requiring a footnote has the following format in the sequence shown:
a number followed by quotes and a closing angular bracket >
The text that needs a footnote
html tags that include Footnote.xhtml#
Using your example, this is:
Code:
1">This is some text that needs a footnote</span><a class="nounder" href="9780061807145_Footnote.xhtml#fn2" id="fn_2">
A possible solution to using my plugin would be to use Find/Replace to find each occurrence of this sequence and insert the tag <span class="FNOTE">..</span>. Then you would be able to run my plugin to generate the footnotes.
Use the following to do this:
Code:
Find: (\d)">(.*?)<(.*?)Footnote.xhtml#(.*?)>
Replace: \1"><span class="FNOTE">\2<\3Footnote.xhtml#\4
Make sure that you select Regex as the search mode.
This will leave the section href="9780061807145_Footnote.xhtml#fn2" id="fn_2" in place in case it is needed by other links in the book eg the contents page, if any. If you do not need this then you could modify the search criteria to remove this. section too.
After doing the search and replace run the plugin and it will produce the footnotes in its standard format.
You will need to do another search and replace to remove the unwanted existing footnotes.
I hope this helps to resolve the issue.