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
Oh man thanks for that, i didnt even know there was a Sharper version of this, I wrote on that post asking them if i can have the footage that would be amazing, thanks so much for pointing this out to me bro