Is there a blender UI addon that highlights the active menu the mouse cursor is hovering over? From what I understand so far about Blender, wherever the mouse cursor is hovering over, it becomes the active region.

Currently, Blender slightly changes the tint of a menu's header as you hover your cursor on and off from the menu. But that small change is barely noticeable.

Is there a blender UI addon that can let the user create a custom color for both the active and non-active Headers or active/non-active Window Backgrounds?

It helps to know what is active, especially on large high resolution monitors.
You can just customize the theme in User Preferences and choose the colors to your requirement and then save the theme as well as make it the default.

Press Ctrl+Alt+U to open the User Preferences and then goto Theme tab.

Customizing Blender Theme