Toyota,
You are headed in the right direction, but your inexperience with LV shows.
First, try to avoid placing icons on top of each other. The HP34401A GPIB Write functions are stacked in such a way as to make it impossible to understand what it going on.
Second, LabVIEW uses dataflow to define the order of operations. The Sequence stucture in the Keithley loopcan be eliminated by wiring the error clusters.
Third, I do not understand exactly how you modified the Despiker VI. It appears that you have two outputs and no inputs.
I do not have your equipment so I cannot run the VI. From the structure of the VI it appears that it will behave like this:
Outer loop (Stop5) starts. The Stop5 button is read. Since it is false, the loop will stop when all nodes inside it finish executing. The voltage setting loop (Stop2) starts, reads the value of Stop2 (false), sends the first value to the voltage supply, waits 1 second and stops. The large inner loop (Stop4) starts before or after the Stop2 loop (certainly no later than microseconds into the 1 second wait), reads the Stop 4 button (false), writes to the 34401, and starts the HP and Keithley loops. The Stop4 loop will stop as soon as the HP and K loops finish. Both of those loops will stop at the end of their delays (1 and 5 seconds, respectively). The waits run simultaneously (approximately).
So, you set the voltage to the first point, read the HP once, read the Keithley once, build tables and graphs with one data point (plus stored data from the despiker), and exit after 5 seconds.
I think you may want to look at a state machine architecture for your program. It would have one loop (or two if you use a separate one for the user interface) and would have states like initialize, write voltage step, read HP, read Keithley, wait, update graphs, write to file, Reset voltage to zero, and shutdown.
Look at some of the examples which come with LV and the Design Patterns which can be found at File >> New.. >> VI >> From Template >> Frameworks >> Design Patterns >> Standard State Machine. This is from LV 8.2, but earlier versions have similar examples.
Lynn