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@nookhoney - welcome to MobileRead.
For #1 it depends what you are after. You cannot change the structure of how calibre stores books in its own library, there is a sticky about that in the Library Management subforum. You can however set whatever structure you like when you export from calibre by setting up the template in Preferences -> Saving books to disc in the Save template. Any questions concerning this you should just ask in the Library Management subforum.
For #2, not quite sure what you are after but there are a few things that might help. There is a feature in calibre we call "metadata jackets" that insert a special page at the front of the book detailing the book summary, series info, rating etc. You can insert this either when doing a conversion (Under Structure detection, tick "Insert metadata at start of book") or use the Modify ePub plugin which has an option to do this without requiring a conversion. In addition if you want the title of the book to reflect the series it is in, you should look into Metadata Plugboards, there is a sticky in the Library Management subforum.
For #3 again you can do this already - go to Preferences -> Saving books to disk and uncheck "Save metadata in OPF file" and "Save cover separately".
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