The best and easiest way to make sure you have the pushrod in the correct location on the brake pedal arm is to pull the brake pedal assembly out from under the dash and mock up your manual brake plate on the brake pedal assembly once it is removed from the car.
To remove the brake pedal assembly, unbolt the four nuts/bolts on the firewall that is holding the manual brake adapter plate and one 13mm bolt that is attaches the brake pedal assembly to under dash bracing. It is located strait up from the floor of the car looking up under the dash, strait up toward the top of the dash. It is usually blue in color.
Off the car, bolt your manual brake adapter plate back onto the brake pedal assembly and then bolt your master cylinder to the manual brake adapter plate.
Lay the brake pedal assembly with the manual brake adapter plate and master cylinder on its side with the brake pedal in the unpressed position against the brake light switch.
Take your pushrod assembly and insert the pushrod into the back of the master cylinder. With the pushrod coming strait out the back of the master cylinder, making sure that the pushrod does not angle up or down coming out the back of the master cylinder, mark where the centerline of the pushrod intersects the brake pedal.
If the pushrod intersects where the PM stud is located then use the PM stud for the brake pedal pushrod assembly. If not, drill the appropriate sized holed in the center of the side of the brake pedal arm where the centerline of the brake pedal pushrod intersects.
Measure multiply times before you drill to make sure the hole is in the correct location on the brake pedal arm.
For the brake line, you should be able to find an adapter that will work. I am not entirely sure what master cylinder you are using, but your front brake line (plumbed to the rear brakes) is, somebody correct me if I am wrong, 9/16-18 and your rear brake line (used for the front brakes) is a 1/2-20. If your front outlet on the master cylinder is also a 1/2-20...
Use either Edelmann part number 258306 - Hydraulic Brake Fittings, Adapter-Standard to Dual Master Cylinder, 3/16" (9/16-18 thread) Female Inv. Fl. Seat, 3/16" (1/2-20 thread) Male Inv. Fl. Tube
OR
Edelmann part number 258306 Hydraulic Brake Fittings, Adapter-Standard to Dual Master Cylinder, 3/16" (1/2-20 thread) Female Inv. Fl. Seat, 3/16" (9/16-18 thread) Male Inv. Fl. Tube
depending on which end is which.