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If you have the modified version of ros_control in your workspace alongside the pakage you're trying to build, catkin should do this automatically (this is one of the core design goals of catkin).

Do you have any output from the compilation process (other than the include path order) that indicates that it isn't using your custom headers?

You could try adding an #error preprocessor defiintion in one of your custom headers to confirm that it is being included properly.