Hey man, good work on the BLACK secondary objective spotting. I actually worked on Black and thought I'd spoil your fun by helping you out with some of the ones you didn't spot. I didn't directly come up with any of the objectives myself but I heard most of them being discussed.
The Phone List for JJ Directorate
This I believe is a reference to "K Directorate" from Alias. They changed it at the last minute to avoid legal issues
Infrared Photographs of Global Thermonuclear War
This is a reference to the film "Wargames"
A Security Pass for Hays House
"Hayes House" is the name of the office building where Criterion software is located
Dossiers marked Operation Take Away
I'm not sure about this one, but the guy who made up the objectives is a big fan of an Indian takeaway in Guildford called "planet spice" ( which incidentally is actually mentioned in the credits! )
A design Document marked “Dust Storm”
Black was originally known as "Dust Storm" when it was early in design ( due to the particle effects! )
The true identity of Master Rodis
This refers to "Nilo Rodis" who was loosely involved with the story of Black. Apparently he was also the guy who designed the speeder bikes from return of the Jedi
Proof of Death of K B Baer in 2001
This is most likely a reference to Jack Bauer from 24 which everyone was into during the development of BLACK. They probably changed the name to avoid legal problems