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Hi Jim,
I have the same issue and have modified the xpml2xhtml.py to handle footnotes when converting to html in another way. It literally now includes a page break before each footnote and and adds a "return" new hyperlink to take you back in the text to where you first clicked on the footnote. It also lets Tidy handle the funny chars so no cleanup necessary.
This works well since only 1 footnote appears on a page when you click on it (similar to how my ereader program handles them). The return link is nice if you have an e reading device that does not keep an any to access page history (ie. read that the Sony eBook reader).
There are also a large number of xhtml fixes and thing. You might like to try it and then let it import the xhtml it generates into Calibre directly (since xhtml seems to be Calibre's internal format).
Anyway that is what I do.
If you want it I will happily post it for you (since it has no DRM removal code ii it at all).
Just let me know,
KevinH
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