So on my 5.0 swap V6 1999 'stang, I'm thinking of cutting out the fake scoop to make a real hood scoop( because that is just cool). Would I have to do anything extra beside cut out the metal?
The only thing a real hood scoop does is ran dirt and water down on the engine. It offers no cooling benefit since it would need to be 2-3" higher than the hood to see airflow. The high pressure caused by the radiator inlet usually prevents much air from entering anyway.
If your reason is for cooling, a cowl hood with the opening at the rear open would be more effective as the low pressure zone at the base of the windshield tends to "suck" air from under the hood out.