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1) In an epub book can I "goto" a specific page number? If not, can I jump forward a bunch at a time (and backwards)? Is there anyway to navigate through a book other than one page at a time?
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No GOTO PAGE feature just yet... we're hopeful it will be added in a future firmware update. Your only other navigation choice, besides page flipping, is the Table of Contents.
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2) Do you allow, or is their 3rd party software, to view books directly through the folder structure. I currently own multiple ereaders and use this feature extensively. I have all my books stored on my reader by genre / author / series / title (incl series #). I use the folder navigation far more than I use Books by author or title. Is there some way to do this with the Kobo?
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Yes. You can use drag'n'drop with the Kobo.
EDIT: It comes to me that I might have misinterpreted your question. The Kobo only has sorting by Author or Title: You can store the books in whatever folder hierarchy you wish, but navigating through the library on the Kobo itself is limited to Author/Title sorting.
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3) I use Calibre extensively. I have a library of 2500 books where I have recorded the series and series number for all books where appropriate. If I wanted to read my Alex Cross books starting with the first one in the series (written by James Patterson) how would I find it on my Kobo? Obviously I don't know the title of the book just that I want the first or second in the series.
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There is no 'collections' support on the Kobo yet. What I usually do is use the 'Create Catalog ... ' feature of Calibre. If you use the TOC and jump to the section that lists 'books by author' alphabetically, it will group series into a nice numbered list for each author.
The only other way would be to edit the titles of your books (eg, Mistborn 1 - The Final Empire, Mistborn 2 - The Well of Ascension, etc)