https://www.fimfiction.net/story/418440/those-forty-years (The sequel is out! Check it out here. Check out my latest blog for why it's on my co-author's profile instead of this one.)

A legendary magical discovery leads the protagonist Twilight Sparkle through a chain of events that not only explain Celestia and Luna's history, but a history about herself that even she could not have imagined.
Co-Author profile link.

WE HAVE COVER ART! 8/3/2016 Check the source for the artist. (permission was given)