As you have determined, the path planner figures out where to move the end effector based on the positions of the parts, which you parameterized based on user input. That data enters the path planner at "CamData Pos" input to "Planning and Control" subsystem.
If you want to influence the wait time and sequence for the end effector, you will need to modify the path planner code in "Planning and Control/Path Planner". You can see the sequence in the switch statement of nextMarker.
Altering this sequence, and perhaps inserting a delay in "gotoPosition" within the same function will alter the behavior to match what you are trying to do.
--Steve