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@heeby - you don't have to rename the books to get them to show in series order. Look at the metadata plugboards sticky thread in the Library subforum - it has the instructions you need to ensure the titles include the series information for sorting without wrecking your title data in calibre. So for instance you could do as I do of collections per author, with titles sorted by series within.
@Ferrian - the modifications for margins etc are not calibre files, they are managed through a system file belonging to the Kindle. Do some googling and you can find the details, there are wiki pages how there for instance describing how to change the margins on your Kindle. I would imagine just doing a factory reset of your Kindle will ensure everything gets back to its defaults if you can't be bothered with tracking the info down, though of course you may need to reload your books etc.
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