Hey Sky_,
here are a couple threads that you may or may not have seen where others have tried to clean up the deleted scenes. You might be able to find some info on how they did it on these threads. Also look into avisynth to clean dirty frames.
https://originaltrilogy.com/topic/Star-Wars-Deleted-Scenes-Reincorporated/id/13512/page/9
https://originaltrilogy.com/topic/cleaning-up-dirty-frames-for-scenes/id/14044