After thinking about it, I came up with an idea. This is just an idea though! You could just take a drill and drill out the holes on the honeycomb plastic that covers the opening on the hoodscoop. Then, you would have to cut your hood under the location of the hoodscoop to make it functional, maybe put some weatherstripping on it so the edges dont rust. Something like that may work. The only functional scoops I have seen for the 99+ is the Shaker Hoodscoop from Classic Desgin Concepts. I know that Banshee (sp?) Performance makes a functional ram air hood scoop for the fox body stangs that looks more like the stock hoodscoop on the 01+ GT. I dont know if they make one for a 99+ GT though, maybe you can look into that.
As for the sidescoops, you would have to cut into the quarter panel for that. I think Classic Design Concpets makes functional sidescoops as well. They look pretty awesome! Hope this helps, good luck with your project!