From the 429 Megasite.
Correct Exhaust Tip Positioning
We believe the positioning of the chrome tips shown in the photos above is the correct factory location. They are close to the valence cut-outs at the tops and sides of the tips. Also, the length of the tip sticking out beyond the valence is correct too.
Additionally from that site:
Exhaust Tips
These are the chrome exhaust tips that came on 429 Mustangs (Part # D1ZA-5202-BB and D1ZA-5203-AB). The original right and left exhaust chrome tips, and their original tail pipes, had indexing features on them so that just the right hand chrome tip fit on the right hand tail pipe, and the left hand tip fit only on the left side. This was done so that the tailpipes clamp screw point, pointed away from the gas tank and not towards it. Original chrome tips were a right and left assembly, and had two different part numbers because of this.