you could also just chop off the end of the header as short as possible put in a cat with a bung before it and get custom piping to connect to the flex and back.
so you wont have to extend that far, but replacing the cat would be a PITA.
so on second thought focus newb you're right with putting it after the flex. the only thing is we don't know for 100% sure that the flex will be able to survive without the cat in front of it.
I still have a Focus parked, I might fix it up one day.