I think my fix is almost done (for SP).
I started playing with trying to center/correct the aspect-ratio of the movies that play and I found a value there that fixed the scaling on my objective text and other little popups that appear (like pressing C to crouch).
I also managed to (kind of) fix the movies.
It will shrink the movie and display it correctly on the left monitor, and continue playing a stretched version behind it on the other two monitors. I've only been testing everything in 3x16:9 aspect-ratios, though, so I'm not sure how it would look at 3x16:10.
I'll work on multiplayer after I mess with SP some more. I may go ahead and get these changes pushed to SVN soon.
As for the HUD, I managed to fix that after talking with HaYDeN. In the earlier CoD games the HUD was always being read from, so you could just start a game, sit there, and start playing with the values you find and watch the changes happen on the fly. With Black Ops II and Ghosts, the HUD position is read before you load into a game, so you have to make your changes first, start a game, see if anything has changed, quick back to the menu, repeat. I'm not as good as finding this stuff as HaYDeN is so it's taken some time.