Just through playing in uncharted 2/3 its safe to say that the journal is indeed a navy/dark blue.
Also I've finally got to the stage where I am about to begin staining all the pages of the journal a light sepia water mix. I have already tried one page at the back and can confirm Your exccelent technique.
I added about 10 or 12 drops of acrylic sepia ink into a diffuser already with some water in (see image below for final result) and then spray the mist onto kitchen paper, or toilet roll (If you use toilet roll I would suggest changing to a fresh clump frequently as the water will cause it to tear much quicker than kitchen roll) Then carefully smear your kitchen/toilet roll across the page (this works well if you mixture is very light i.e not a dark sepia, just a light tan) then once you have done that and the page dried you can dab the page in certain areas for a better result and a more aged look.
Also Darth I'd be more than happy to work with you and any others to create a replica of drakes journal from Uncharted 3. Im actually contemplating combining the two into one "mega journal" as from what I can tell the jornal nate uses in U2 is the same one he uses in U3 (going by colour at least)