the scratches on the wheels inside the holes where the lugs go - you can't do much about those. i'm a ford technician and i try and be as careful as possible when i rotate the tires on my X but i still get those scratches from my sockets. the holes are just big enough to fit a socket in there - thats why they scratch. a lot of wheels get that on them.

as for the window, that's up to you whether you like the way it looks or not. IMHO, i think it doesn't look good b/c the other windows, especially the back 2, don't have weatherstripping around them.