Just for grins, stick a screw driver up to the inside edge of the metal of the pad and work the pad back into the caliper. (spread the pads back into the caliper) (carefully) then go to the pedal and pump it pack up. When mine starts to go too far down that's what I do and it puts the pedal right back up to the top of it's throw, works for me! I like having brakes within the first 1/2 inch of pedal travel. You also need to know that if you adjust the rod, you must leave some (tiny bit) free play in the mastercylinder so you don't close off the compensating port, which will cause the brakes to drag and/or not release when you let off the brake. "Don't make that mistake"