The chopping of pages is normal for anything converted to pdf by Calibre. The Calibre conversion to pdf uses the QPrinter part of QT and that always chops to size.
To avoid that problem I have been converting to the htmlz format and then using Firefox to open the index.html file found after using unzip on the htmlz. The Firefox can then print the index.html to pdf. Firefox reformats the html before printing where the QPrinter just chops the browser display to size without being reformated.
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