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The lighting on the recent Claras is as good as it gets right now IMO. And no, there isn't a way to get the page numbering to be consistent without switching to an older firmware version (it was changed along with the new reader recently).
For Calibre, KoboTouchExtended is essential if you want to use the kepub reader (it has faster highlighting, better stats, pop-up footnotes, faster page turns, and a bit more compared to epub, whose only advantage is better typography). If you don't use Calibre, kepubify is another option.
Kobo does support nested table of contents. To make it more noticeable, have a look at the patches.
For Kobo tweaks, a good place to start is with the patches. I'd suggest looking at the ones in nickel.yaml and the header/footer ones in libnickel.so.1.0.0.yaml. You'll figure out which other ones you want as you use your Kobo more.
If you want, you can also play around with koreader or plato. Have a look at those threads for more info.
Also, in the future, you might want to split your post into paragraphs instead of having a big wall of text.
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