Why are you creating a new DAQ task for the digital output within the loop itself on every iteration? That Create task belongs before the loop.
You have 3 arrays that you are building continuously in shift registers. As they grow, the computer needs to find ever larger pieces of contiguous memory to store those arrays. I'm surprised you are having problems after only 30 seconds, but not surprised you are having the problems ultimately. I bet the reason I listed above is the reason it is happening so fast.
Try using the producer consumer archtitecture to pass the values off to a parallel loop and write the data to file condinuously there.
I see in your instructions you are telling someone to hit the Abort button to stop execution of the code. That is always a bad idea. You should design your program as a state machine where you have different states for running and setting up different parameters. A user should never hit the Abort button (you will fail to clean up tasks properly.) And they really should never need to hit the run button either once the application is compiled into an executable.
