Peter,
Do a search on this site for ride height, front suspension, and rear suspension. There has been lots of discussion on setting these cars up correctly. Rick Bagley (Eliminator) is one of the resident experts on shocks and springs.
One common theme you will see in nearly all threads is this...Set the suspension up based on ride height and corner weight, then move the body on the car. Adjusting the suspension to compensate for appearance may get the "look", but it will kill the handling. These cars, like the real 60's Cobra's, are not symmetrical nor exactly the same!
Building our car we literally took an entire day to set the rear end up square to the frame, then adjusting toe and camber without any reference to the body location. Good luck!
Brian Carlson
Unique 9122 - 289 FIA - 351W with 8 stack EFI - Formerly known as the "Legendary Spence Car"