I don't know what section you could cut out. It's all so rich. Unfortunately, the rules confine the running time to 30 min. I believe to obtain the rights is to also agree not to change or cut ANY lines without consent from the Beckett estate. Such permission, I have heard, is next to impossible to obtain.
Endgame is so bare and carefully arranged as it is.
Beckett did all the cutting necessary before it was published. I don't know what section you could cut out. It's all so rich.