Your springs should settle after about 10 miles of driving enough to take accurate measurements.
Measurements to check:
1) check tire pressures and make them even (and set them to the pressure on your driver door sticker)
2) Are your wheels and tires the same height all four corners? Same wheel size? Even tire wear? Same tires all around?
3) check on a flat surface ( must be completely flat!) - what are your floor to fender heights for all four corners? This is what it should be stock measuring at the center cap of the wheel: 27.5" front, 28.25" rear. Subtle differences in slope of your surface can make a big difference (my rear measurements are the same on a flat surface but when I park in my driveway they are 3/8” different because of the slope of my driveway - but I can see that the bottom of the rear lower arms are at different heights and the driveway has a clear slope when I put a level on the ground)
4) the springs are built assuming your weight distribution is stock - if you have taken out your spare tire or weight from either end or if your trunk is full of speakers / other equipment this will affect how your car sits. (Your issue would be there is an increase of weight in the rear compared to the front from when your mustang was stock)
Fixes:
1) worn spring isolators or a lack of isolators can make subtle differences
2) Properly index your springs. If you did the install you should have noticed that the last coil sticks out a bit farther, make sure that last coil is oriented the mirror of the other side (for front arms make that last coil face out from center line). Clocking of the springs is often over looked, be sure to index the spring, both left and right, in the same direction. This will ensure the car's ride height will be even left to right and front to back.
3) do an alignment - settings should be 0.5 neg camber, 4 positive caster, 0.5 toe-in: read this for more:
http://www.maximummotorsports.com/assets/install/pdf/front_susp/MMCC9994v4r8.pdf
4) if there is any prior car accidents / body damage this could result in what you are seeing. Check a carfax and consider a body shop evaluation to check for prior damage.
5) if none of the above work consider different springs (or coil overs) with different drops to get the look you want.
