Here are the files for the Battery Charger. I tried to clean them up some and make it more readable (it's not perfect), however some errors may have been introduced in the process. Also some of the parts have been changed throughout the course of this project, but if they had the same footprint I didn't bother changing them in the schematic Often there are several parts you could use, the only one that matters is the temperature sensors. If you open up the schematic in Eagle and click on the temperature sensor it will say it is the LM62, but in the final design I ended up using the TC1047A. This makes a difference in the firmware because the TC1047A has a Temperature Slope of 10mV/°C, whereas the LM62 has a Temperature Slope of 15.6mV/°C. Other than that if you use the part listed you will be fine (or you can pick your own parts).
A manual is being put together for the latest version of the firmware and I am making a tutorial to show you how to upload it for those who need it. I am also working on a dedicated page for this charger on my website so that all the info is not just buried in my blog.