The two sets of holes do need to line up (inner-to-outer cowl and rocker). See the last picture I posted. The larger hole is for the shaft and the smaller holes are where the support bolts on to the rocker. The Parking brake pedal shaft also has a bracket that bolts to the floor support, so that's another spot where you can check the alignment. I believe the pedal shaft should be perpendicular to the vehicle centerline when installed.
