Years ago, someone asked me if I knew anything about a new edition of the Gideon Welles diary. I didn't, but this summer 2014 release -- The Civil War Diary of Gideon Welles, Lincoln's Secretary of the Navy: The Original Manuscript Edition edited by William and Erica Gienapp (Univ of Ill Press) -- is surely just what that person was looking for.
I don't know anything about this diary's publication history but this statement from the upcoming volume's description "In this new edition, William E. and Erica L. Gienapp have restored Welles’s original observations, gleaned from the manuscript diaries at the Library of Congress and freed from his many later revisions, so that the reader can experience what he wrote in the moment" seems to indicate that previously published versions (the 3-volume 1911 edition?) were contaminated by post-war editing.
[Postscript 4/24: Paul Taylor posted about this very subject back in 2008. Go here to read it]