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css handling has already been changed in calibre, but those changes wont be released until 0.6.0 If you're comfortable using the development version of calibre, you could check out the new code.
As for chapter detection, chapter detection works the same no matter what type of source file you have. You just need to adjust the XPath expression accordingly. And note that calibre split HTML files on page breaks not neccessarily on chanpters. By default it inserts page breaks before chapters, so you may not have realized this behavior.
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