I ran the sample VI you have and it seems to work fine. I can not run your main VI because of missing VIs and HW.
To modify your original VI all you need to do is add one more shift register to store the 1D Position Array. So just like you create "Array" in your main VI do the same with the "Position Read After Motion"
You can then use those 2 arrays just like you do in the example VI and you should get a XY graph that behaves like a chart.
This should be ok as long as number of steps is resaonable small. Also every time you hit "Acquisition Go" it will clear out the graph due to the inititialized shift registers.
