I can see you are making good effort for the next update, glad my feedback can help.
One suggestion for anatomy if you are just starting out to deal with it, it is to use reference, pose for the exact pose for a photo and use it with modifications to the anime face, it will come out more natural looking.
300 backgrounds are indeed a looot of work to modify, I say start with the batch the story would use the most, with the most repetition, the go rooms were fine but bus stop area, the white building, look for bgs with strong contrast and tone it down as priority. Your least distracting ones are the 3D generated bgs of the spaceship, those are fine you don't need to touch up.
