The protective film did what it's supposed to do, protect the paint from chips and stains. Nothing will take out all the stains in the plastic film. You could try a magic eraser with some Crud Cutter, but that will likely discolor the film. Only recourse is to replace the film, which would require removing all of it, which is a bit-h.
Never could see using the film. With paint or gelcoat, bugs come right off, and front cap is high enough that I don't worry about chips. That's also the nice thing about having plain white and no full body paint. I don't fret about every little nick, chip, or gug buts.