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1) Use mostly semantic markup in conjunction with CSS for styling and you'll have a good balance between the book's structure making sense and looking nice.
2) Yeah, if it's superfluous to an e-book edition, and doesn't mess with the meaning of the main text, you can get rid of it. One nicety to replace print index pages for specific subjects is to look up where it indexes, and link back to that piece of the text, but that tends to be a lot of work which you may not want to go to the trouble of doing.
Sometimes the search function can be overly literal and only give results back for a particularly-spelt keyword variant. Or sometimes it does partial matching and then the results are overly broad and you have umpteen pages of pier, Piers, piercing, rapier, happier to wade through.
3) Go ahead and add whatever you like. But as in the case with deletion, it's best if you can make it clear it's not quite the original text by adding some sort of note in the front of the book saying "I sourced this from SOURCE and made the following described modifications to create this e-book version which should be considered The Ficbot Super Special Edition of Adventures in the Public Domain, or, a Thrilling Tale of Textual Revision".
Excepting Project Gutenberg texts, whose boilerplate says that if you make any changes to the text besides making them more readable on a display device and cleaning up obvious OCR errors and prettying-up the typography, you have to completely remove any mention of PG from the result.
Mind you, for your example of the reference, possibly it may be better to directly link it back rather than quote a line of text that people would then have to enter into a search box on their reader (assuming their reader comes with a search box, which I'm pretty sure Kobo doesn't; but then Kobo still doesn't follow internal links, so the point is moot for that device).
Hope this helps.
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