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Unfortunately I can't speak to Questions 1 and 2. However, I've had the same problem as you with #3. It usually seems to occur with books that have images at the start of each chapter -- I believe the height of the image pushes the text down just far enough to obscure the bottom line of each screen. I haven't tried any of those problem books with the new version of Stanza -- it's possible that they fixed it. I do think it is a Stanza rendering glitch, not a Calibre conversion bug.
The one recommendation I would suggest (which I haven't tried) is to open up the Calibre-generated ePub file (it's essentially just a zip) and modifying the raw HTML to remove the references to the images.
Then again, if images aren't your problem, then I apologize for wasting your time :-)
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