You should have a return spring on your brake pedal, so that after you apply the brakes and then take your foot off the pedal, the pedal returns to a "no brakes on" position. There should be a positive stop to prevent the brake pedal from returning too far, or yes, your brake actuator rod that goes into the master cylinder will indeed "fall out". The correct way to set things up, is to have your brake pedal held in position against this "positive stop" by the return spring, (brakes completely "off"). The clevis end of the "brake actuator rod" is attached to the brake pedal "lever" . Loosen the jam nut next to the clevis, and unscrew the rod untill it is seated in the back of the piston in the master cylinder---not seated hard enough to actually move the piston, just in contact with it.---Then turn the rod back the other way about 1/2 turn. Then tighten the jam nut against the end of the clevis. Now the rod can not fall out, because the pedal can't move back any farther (remember, its against the return "positive stop"). There are about 400 ways to make a "positive stop" for the returned position, ---one of the easiest being a spacer welded to the top side of the brake lever that will contact the underside of the floor.