Thanks for the warning Toxaris. Fortunately, a Kindle 3 now seems to read the azw3 file well (converted from the epub). Hopefully, the Javascript will stay as "extra/ useless" but not harmful content... The links to footnotes too work as well... Thanks to Jellby again, this may be very useful as that html pattern is present in not one but many online html books. I may need to learn a bit about regular expressions to make the cleaning faster but am glad to know that there is a good chance the end result will work on Kindle...
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