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I got this thing working now. I followed this : Similar Question

The key was that I had to rebuild all other packages also which were dependent upon OpenCV (vision_opencv which has cv_bridge). Also, in my cmakelist file, I have include all OpenCV packages and libraries for my project before the catkin packages. I dont know currently if it played a major role, but atleast its working now.

If the problem still persists, please check your $CMAKE_PREFIX_PATH and $LD_LIBRARY_PATH. They should have the /usr/local (where your custom OpenCV is present) path before any of the ROS paths.