Copy Hydro (ROS-Comm) from another drive

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I had to reinstall my Ubuntu 13.10 but am able to recover files from the previous hard disk. Thus I am trying to set-up my ROS Hydro install (ROS-Comm compiled from source) by copying files across due to a poor internet connection. So far it seems to be working with some exceptions. I can create new workspaces, create packages, catkin_make packages, use roscore, run publishers and subscribers. But what is not working is the preprocessor that converts msg and svr files into C++ header files (and probably same problem with Python/Lisp files).

From Installing on Ubuntu from source, I performed the following steps:

sudo apt-get install python-rosdep python-rosinstall-generator python-wstool python-rosinstall build-essential
sudo rosdep init
rosdep update

    copied my ros_catkin_ws

copied entries from my old .bashrc to current one (including necessary environment variables):
  source ~/ros_catkin_ws/install_isolated/setup.bash

rosdep install --from-paths src --ignore-src --rosdistro hydro -y

Tests:
  roscore   (WORKED)
  rostopic list (WORKED)
  catkin_make (WORKED)
  ran my publisher/subscriber nodes (WORKED)

I'm wondering how the preprocessing takes place, and hence what I need to fix up. Could anyone please elaborate on this or point me to a reference I can read up.

Thanks, Nap.