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1. ToC on Kindle will show page numbers, if the book has page numbers that is. All it takes is the .apnx sidecar file which is on all Amazon-downloaded books, and calibre can create a rough guide as well.
2. Bookmarked pages. Well, you'd have to deliberately mess that one up. I can confirm Amazon didn't mess it up. Tap on a listed annotation on the annotations list, and it opens.
3. List all annotations. Well, all annotations when created are added to a file (appears as a "personal document") called "My Clippings.txt" but if you sync the annotations from your other kindle, they don't get printed to this file.
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