The box should lay flat against the bracket. The 2 brackets that sandwich the frame a about 3/4" total thickness. Sometimes the casting marriage line on the box is thick, double check that and also make sure there aren't any bumps on the frame that are causing the box to push away from the bracket. Here is an install story on the CPP kit, in case that will help out:
http://www.classicperform.com/tech_a...tOldSchool.htm