The system works, and just in time. I'm sure I will continue to expand this at a later date, and there are definitely a couple areas that need some work. That said, I think the core concept is good, and is useful as a design philosophy for systems like this. 

The basic idea that drove the entire project was that the integration of many systems could create something useful, and I think that has been shown to be true. The wake-up routine is useful, and shows important sleep data. The light switches allow the system to be accessed in an intuitive way, but also allow the living room lights to be turned off from bed if forgotten. 

The interface was deigned from the ground up to look like something out of Tron, and I think I succeeded in that respect. The voice commands are more Iron-Man, but I'll let that slide for convenience's sake.

Notes:

It wasn't specified in the project logs anywhere, but the sonic screwdriver worked as expected with the replacement switch. The only tricky part was that I needed to configure another Arduino to blast the signals to train the thing because, although it has a USB input, you can't actually program over that, it's just for power. Just keep that in mind if you want to do that.

A 3D printer isn't strictly necessary for this project, but it helped to make the enclosures look more like I wanted them (Tron-like). If I did it again, I would likely try to use natural PLA in a second extruder to get the trademark circuit lines in the parts, but, alas, I didn't have one.

It's unfortunate that configuring the Android app is so difficult, but that's how it had to be for the look I was going for. Procedurally drawing that based on a line drawing was going to be too much work, so I took the shortcut of just drawing it out in Inkscape/Filter Forge by hand.

In this entire project, the hardest part was getting those SparkFun RF transponders to work properly. I ordered antennae specifically designed for 315 MHz, but they didn't make too much of a difference. The packets eventually get through, but the packet loss rate is crazy (easily 75%). That is a good argument for upping the cost of the system by a bit and going with standard Wi-Fi or Bluetooth, but that has its own set of problems. Suggestions on this point are more than welcome.

Future improvements

Opening the blinds as part of the wake-up routine (The machinery for this is more or less in place, but needs a bit of extra logic to make it work)

Making coffee in the mornings (I would have put this in for release 1, but if I broke the coffee machine I would whither and die, and nobody wants to clean that up)

Bugs:

There is a 1-5 second delay between flipping a light switch and seeing the result.

The integrated switches rely on detecting power from a wall socket through a wall wart, which, when combined with the packet loss from the cheap RF kit, causes an unacceptable delay (especially when turning the light off, as you have to wait for the wall wart to turn off completely). The solutions I see are increasing the power of the transmitter and switching to a faster way of detecting outlet current.

Also, I haven't forgotten about the bonus hacks (though neither of them are as cool as the 6-monitor mount). I'll put those up later today (Can't get good pictures of the lights when it's light out).

Special thanks to my girlfriend. Her suggestion on how to improve the system, as well as her keen eye for deign, made this system look a thousand times better than it would have (she would be listed as a contributor, but she doesn't have an account here). Also, she should be nominated for sainthood for not killing me after the fiftieth time I broke the lights.

Also, thank you Colabot. Without your collaboration, I could not submit this project without roping in my already-swamped girlfriend.