1. Yes. Find out where MobiCreator puts the project folders. Open the html file in that folder and edit that file. Save your changes and then remake the ebook. So long as you don't try to save while making the ebook you won't have a problem.
2. Yes, but you'll need to make the list of links by hand. And if you want to have the lists under the goto menu, look into the "guide" area of mobicreator.
3. I usually use MobiDesktop or some other Mobi viewer on my PC. I only use the Kindle for the fine tuning at the end.
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