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There's a lot here so I don't know whether you've got your answer yet or not, but I don't think anyone has said these steps explicitly. The installation requires you to uninstall the pip version if you're running Ubuntu (and trying to install ros-groovy). So follow the installation guide normally up to this step

$ rosdep update

Then if you get the error again after reinstalling Ubuntu (which you said you're doing in your final edit, however that should not affect anything), call:

$ sudo pip uninstall rosdep

to remove the pip version, then try again with

$ sudo rm /etc/ros/rosdep/sources.list.d/20-default.list
$ sudo rosdep init
$ rosdep update

Hope that works