Windows don't scratch because of fingernails..... but,
If it's a true surface scratch, you have a couple of options 1) is to go visit a local glass shop (any type - house, car, etc.) and they will be able to put together a polishing kit for you..... basically a cotton buffing pad that can attach to the end of a drill and glass polishing compound...it's in a powder form. Low speed, light pressure and patience will take care of that.... but work slowly because if you go too far (so to speak) you can get "waves" in the glass...and that is not repairable. 2) A glass shop can polish this out for you 3) Toothpaste has jewlers rouge in it and makes an excellent glass polish as well..... "Pearl Drops" tooth polish is very good for this but any brand will do.
As far as the side windows go, definitely need to remove the inner door panel to see what is going on..... the side "guides" have felt on them and most likely got dirt on them causing the scratches.... clean with a soft brush (toothbrush)….do not use any carpet cleaner or solvents on this!!!!!!! a little simple green is ok if it's grime. Otherwise you might (unlikely) find the felt has worn away and must be replaced.
Member: Never trust a person over 40 who drives a Chevy club
Flatheads ain't so bad!
Certified backyard mechanic I & II