Hi there and welcome to the Computer Hope Forums.
Hope you become a regular here to get some answers (and, why not?, share your own information with others).
Coming to your problem...
Save the text file as a batch file. That is, change the extension to .bat instead of .txt. You need to have the extensions visible to do that (one way of showing extensions: open a folder > tools > folder options > click on the "view" tab > UNcheck "hide extensions for known file types".)
Then open the startup folder (start > all programs > double click on "start up" folder). Copy and paste the .bat file, or make a shortcut and put it in the stratup folder. That should execute your .exe file when the system boots up (and user setting starts to load).
this is to ensure everytime the system reboot will resume back the script
Did you mean current progress is saved and at reboot it continues from where it left off? In that case, I'm not sure how to do that.
Hope this helped
Two-Eyes %