I just wanted to update everyone that after some private correspondence with gromitdj, I got my setup working.
I started with a fresh installation of raspbian weezy, and followed these instructions
http://docs.brewpi.com/manual-brewpi-install/manual-brewpi-install.html
At section 4. "Using Git for BrewPi", after running
"sudo apt-get install git-core"
I entered
"sudo -u brewpi git clone -b legacy
https://github.com/BrewPi/brewpi-script /home/brewpi"
Then
"sudo rm /var/www/*"
and finally
"sudo -u www-data git clone -b legacy
https://github.com/BrewPi/brewpi-www /var/www"
to install the legacy version of BrewPi
afterwards, it was necessary to run the command
"sudo /home/brewpi/utils/fixPermissions.sh"
to fix the permissions of the /var/www folder to allow the flashing of the arduino.
After the arduino was succesfully flashed, I found that I could not install any detected devices until after I ran the command
sudo echo 'E\n' > /dev/ttyAMC0
to clear the EEPROM of the arduino. After running that command, all devices installed properly, and i'm currently making my yeast starter for my first temperature controlled brew ^_^