I purhased a 2006 gt and when I get to anywhere over 65 MPH the hood starts bouncing like its not latched good but it is latched. You can see where it starts to catch air and bow up away from the car along the side. When you hit speeds in excess of 80 MPH it gets rather scary because it looks like its going to fly off the car. The ford place says there is nothing wrong with the hood. I know of 4 other mustang owners that have 2005 and 2006 models that do the same thing. It is definitly a design flaw. Any one else had to deal with this?  

Can you adjust the rubber pad seats to keep the hood from moving? On my 02 v6, the hood would move around quite a bit when I hit 130-140. But tightening up the rubber bumpers and it's ok to about 155. But my functional hood scoop started to get a little squirrly. I've got extra bolts holding that down now. As a last resort, you could try hood pins.