I think it'll be much easier for user to just have 2 separate panel, one for displaying all the jobs, one for jobs that will run when execute the script. Then user can just drag and drop or click a button to add the jobs to the script.
Right now, you have to write the script by hand, which is tedious and error prone (typo etc.)
How about it?
PS: One a side note, can you explain how "Short comparison" work compare to "Full comparison"? I noticed that "Short comparison" is much faster than full, but I don't know about its correctness.