Yes, I prefer shoulder presses over handstand pushups. And regular bodyweight squats are kinda easy so pistol squats are usually recommended as a more challenging alternative. But I prefer to do trapbar deadlifts rather than progress to pistol squats.

Good Luck on rehabbing to be able to do obstacle courses again. I have watched Ninja Warrior on tv and enjoyed it. But I don't think I am acrobatic enough to do a lot of the things I would need to do in order to make it through a course.