This?? Are you sure something is not damaged or loose? If motor is moving check the wiper frames for damage.
As far as indexing goes: The wiper motor automatically stops at a preset point which is at the bottom of the stroke (windshield wipers will be at the bottom of the windshield. The motor should already be indexed correctly. If you're worried about indexing the wiper arms wrong connect the harness into the motor (before connecting into the wiper frame) and turn the wipers on, then off. It'll do a cycle and then stop. Then install it into the frame. Then put your wipers on.