On the actual cars, the difference in the wheelbase is behind the front seats. Mustang Carpet fits in a Cougar.
BTW the engine compartment from the AMT 67 Mustang fits the AMT 69 Cougar nicely. Cut out, clean up the edges, add a couple of strips of Evergreen on the sides and install in the Cougar.
I used the front portion of the Mustang chassis and rear portion of the Cougar chassis in my build. Can't remember where the splice is.