An "accuratized" version of th FJTM might be nice. Accuratizing the exact layout of the Connie interior is problematic, as always, though.
Plus, I would include the missing pages (medical hypo, etc.). New pages should be added for dress uniforms, the first season hazard suits, jump suits, and other ship types seen in TOS/TAS.
Frankly, I would dump the Articles of Federation and treaty wankery (since there's no way to canonically validate it), though I'd keep at least some of the flags.
Also, I'd replace Fleet Headquarters with the STIII Space Dock (in planning stages, maybe).
Just a few ideas, to start with....