Try this: Make a menu only sketch.
Skip all hardware and make the basic menu handler. Let the menu handler call dummy functions like "move stepper", "write to LCD" etc.
When that works, replace the dummy functions with sharp, hardware functions.
Else You will find Yourself lost in a spagetti.
No project like this is like a baby jigsaw, just put down pieces where they fit, and, voila, it works.
Divide the project in parts and attack the parts one by one.