Dang. This was pretty cool!
I'd recommend changing your emphasis in a few places:
1) The hints you give in the menus as to controlling the different applications are a bit overdone and therefore overwhelming. Don't worry - it's quite intuitive, so you can probably strip around 80% of the text. Don't make the same mistake I often did and cradle the work you've already done. Now that you've done that work, you can assess what you should keep. Maybe just keep basic functionality descriptions of each application.
2) The controls are also a bit overwhelming in their descriptions. Find a way to reduce that information through a visual of the buttons, or grouping together similar buttons into a single pictograph to reduce visual load on the player; you don't want them leaving your cool experience just because of some UI!
3) Kill the environmental hints. Things like pointing out the computer code within the light box are a bit much and certainly the most immersion- and challenge-breaking of these three text-overload points. Something like the notebook on the table was nice, as it seemed more naturally a part of the environment.
I'm not sure if the game box was a red herring, an Easter egg, or both, but it was fun to manipulate. I really enjoyed the physicality of the drawers and levers, as well as the sound design and atmosphere combining to form a real sense of interactivity.
Keep going!