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You can add any buttons you like to the viewer toolbars, see the documentation of the ViewerPlugin.customize_ui method on how to do that.
Those buttons can trigger any action you like, including showing a dialog with config options. You will just need to use the standard PyQt QDialog class to create such a dialog.
As for how to store the configuration options, you can store them in any way that you like, just choose a unique name for the config file, so that it does not conflict with the rest of calibre's config files. Use the calibre JSONConfig class to manage the config file easily.
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