@ Thorn
I think that the red box on top of the Carfax Tower has simply to do with the first chapter. And the note is identical to the one you find during the "deadalus" challenge in chapter one. I might be wrong though, although in chapter 4 you definetly won't be using it, so don't worry
@RLB
Spoiler:Have you looked at the photos on the desk in the office? For a second time? Especially at the one with the blue tiles in the background? If not, you have to take that photo (it show the couple drinking at some kind of party), scan it and find something noteworthy...