Although there are several theories, I'm told that the original A&C moulds were splashed off an original Cobra. This would account for the fender to fender differences. Do not try to align the body by looking in the fender walls, you will go nuts.
The body should be pushed all the way up until the rear part hits the axle hump on the chassis. Then do the left/right by looking underneath and the bodies relationship with the chassis. Also, once aligned that way just step back and take a look.
Also, you haven't set your ride height yet so your body may be a bit low and it looks tight.
You will also find that when you mount your sidepipes the drivers side tends to drift in toward the rear fender so your pipe, if straight, looks like it's coming away from the body. You will have to bring it in about an inch so it follows the line of the body.
As far as ground clearance, my Lakewood housing is about 4.5 inches off the ground and is the lowest point on the car. Some have just cut off an inch but I've left mine intact.
Check out my A&C build site at
http://www.priveye.com/cobra.htm
Roscoe