The vertical ruler on the bricks in the photo is on an angle to the camera (see upper-left inset). The photographer (the photo was taken on the 25th) appears to be looking down at a sharp angle. However, this would not affect much the inset ruler on the floor.
"Box D" is another way to approximate a sense of dimension. The box as discovered was resting on its top, so fingerprints were partially on the box's bottom. The box was opened from underneath when they left its contents at the building; the feds only wanted the carton. As photographed at the National Archives, the box end in the 1963 picture is about 11 1/2" wide.
The two pipes pass through the seventh floor uninterrupted and my guess is they served for ventilation, possibly for toilets, sink or the AC. I believe the toilets and sinks were towards the back. So maybe one pipe was for AC fresh-air intake and the other pipe was to exhaust hot air the AC removed from office rooms below.