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If your only trying to get kepub to the device, then you probably just want the KoboTouchExtended driver. You need to make sure it is enable, and, you should disable the built-in KoboTouch driver. This can be done on the Plugins page of the preferences.
In the configuration of the driver, you need to makes sure that "Enable Extended Kobo Features" is enabled in the "Extended" tab.
With this when you send a book to the device, the extended driver will do the work to transform it into a kepub.
It is possible for the transformation to kepub to kepub to fail. The driver has an option to ignore the failures and send the epub as is. If this happens, it usually means there is an error in the epub that needs to be fixed. If you open it in the calibre editor, you can use the error checking to show the problems and fix them.
Your chapter problem with the Witcher book is almost definitely in the source book. The creator has probably split some longer chapters. This is because some ereaders have problems with internal files longer than this. A conversion in calibre usually does this if an internal file is longer than 260KB. The extended driver does not do this, it des not change the internal file structure of the book.
As to which of the plugins are reliable, they all are. They just do different things. The Kobo Output plugin is not needed if you don't convert books to kepub using a conversion. The Kobo Input plugin is used if you have kepubs in your library and want to convert them to other formats. The Kepub Metadata Writer and Kepub Metadata Reader are used to update and read metadata from kepubs respectively. They are mainly needed if you are keeping kepubs in your calibre library. Finally, the Kobo Books metadata source plugin is to fetch metadata from the Kobo store for books.
Which of the plugins you install and use depends on what you want to do. You can happily use none. Or all.
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