They shorted you a piece. There should be a union to join the clevis to the master cylinder rod.
I solved the mis-alignment this way: (from the tech tip)
"I picked up a 2" long 3/8-16 bolt, a nut and lock washer, all in Grade 8. I used the supplied washer and spacer on opposite sides of the rod end. I put my new nut and lock washer on one side of the pedal and the supplied nyloc nut on the other side. Now the bolt is tight on the pedal and the plunger goes straight into the master cylinder.
