Dec. 28, 2015: Oops. Rev 2 files came back and there was a via shorting to a trace. It was a dead power to ground short. It was simple to fix on the boards, but in case anyone else is looking at these files, I wanted to fix it. It's been fixed on the project page by uploading Rev 3.
This marks the end of the project. I was able to get 250 mA out of the output at 5V and 350 mA at 3.3 V. This is more power than an AA can source for any more than 20 minutes or so, so I wouldn't recommend running it this hard. It's been a nice little project, and I'm glad it worked out. It's available for sale on Tindie. Link is in the project description.