I had the EXACT same situation this past summer when I installed
a SSBC front disk brake kit on my '66. All the parts were from the SSBC kit and the pedal was way TOO high. The SSBC supplied pushrod was too LONG and they don't sell shorter pushrods. Pedal height is determined by how far the pushrod (female thread) is threaded onto the rod (protruding through the firewall) which is part of the booster. Even with the pushrod threaded as far as possible onto the booster rod, the pedal was still too high. SSBC suggested that I cut a small amount off the male threaded rod on the booster. I didn't want to remove the booster & MC from the car (brake system was operational), so I cut about 1/4 inch off the booster rod from under the dash! That was tough. Because of the geometry of the brake pedal linkage, that 1/4 inch reduction in the length of the booster rod dropped the pedal to a normal height. You don't want to cut too much off
the rod & lower the pedal too much. You need enough pedal 'travel' to apply the pads & shoes and stop the car in a panic situation without the brake pedal arm hitting the carpet! Sorry for the lengthy post but unless you've gone through this, it's tough to visualize.
PS: I did try a shorter push rod (designed for manual brakes) which is sold by Virginia Classic Mustang, but it was TOO short and I didn't have enough pedal travel before hitting the floor.
Paul E. Floro
'66 Candy Apple Red GT Vert / 289-4V, C4, PS, PFDB, Factory A/C. LOVE ALL MUSTANGS!