I had my friend who was supplying the audio add a reverb to give the feel of it being played in the large open field(Then learned about unity reverb zones as I was working on the project), between that and having to record quietly at night due to limited availability with the jam lead to using what I had rather than getting new audio. There's some small story hints but nothing major for gameplay.
Controls and communicating them to the player is something I really have noticed I fell short on. I modeled the control layout after source games such as Half-Life2 and Portal and hoped that players would be previously familiar with such. This was a failure of judgment on my part and I'm going to have it corrected in future versions. Prompting the player is the plan right now, but I do want to avoid prompting for every cube and so I'm planning on doing more simple puzzles only really involving moving cubes. I hope prompting here will give players a chance to learn control with out having basic gameplay waved in their face the whole game.
The last area I start the player outside a door way that leads into the play area. Design-wise there wasn't any reasoning to it. Really it is just where I had started the player as I was testing the puzzles. I never moved the player when building the level and when having a friend test it I didn't have issues with players wondering off so I just hoped that most players would do the same and I could cut corners there for the jam.
Thank you for your feed back and sorry I left such a long reply, I get really into talking about the process that went into this. I enjoyed creating the whole project so much! I'm working on a patch for after the jam and thinking about doing a postmortem on the build submitted here.