sroxberg,
I have the stops mounted to maximize the overall length of the jig, and the first hole for the base plate will drill @ 80 mm, this puts the base plate on 96 mm centers for the door drilling. I don't use the jig for drilling the doors, its to easy to use a dedicated drill press.
The two pins that stop the rail and position it are needed with my setup, reason being when the stops on the end of the rail are mounted in the furthest position, the locating pin is not used, so the stops will rotate a little if bumped. These stops only prevent end to end movement, so this is NOT a problem, providing you are using the rear locating pins to set the front to back dimension.
Hope this helps.
Mirko