I emailed Fantasy Flights but got no response.

Lets say you score Project Wotan and someone makes a run, the card normally reads.

"trash 1 program

End Run

Would it now read:

Trash 1 Program

End Run

End Run

Or

Trash 1 Program

End Run

End Run

End Run

Is it after each subroutine add End Run

or is it at the end of the card add 1 end run subroutine

It only adds one subroutine, regardless of how many it had originally. If it worked the second way, it would read "after each of its other subroutines".