I watched a video on the c6 corvette about how when the battery is reconnected your supposed to reset the window indexing, does anyone know if this apply to the mustang as it to has window indexing.

My concern is when I put my windows up I can hear a high pitched scrape and on the inside of the glass as multiple vertical lines. I am abke to wipe the lines away and have tried cleaning the inside of the window felt in case it is grit or dirt but eventually this issue comes back.

 

I don't think the two are connected.

You'll know if your window needs resetting (never heard it called indexing, though!) as the window will not go drop when you open the door. You probably know, but to reset, simply lower the window all the way, wait for the click, then all the way up.....and wait for the click.

You issue, though, sounds more like you have a significant amount of grit in the door panel. You may need to remove the door panel to clean the area fully.