Everyone has
Wash and/or replace the pads on the outer door weather strip seals. Or buy a new set depending on how bad the outer strips/pads are.
Once you have done that then every now and then when you wash your Skyline clean those pads. (prevention).
NO you can not polish those scratches out (if someone says you can then ignore them).
They're white long threaded small velvety pads. You can use an adhesive to put them on (cheaper way).
or as I said above get new outer weather strips from JJR, Nissan spare parts or RHDjapan.
Caused by dust, small hard objects and in some cases broken (shatterd) glass.
To remove the strips - wind window down, un do single grub screw (under rubber near the end of the strip, door handle end) and lift from the door handles side to the mirror side. (2-3 minutes effort)...
Cheers
Richard
Edit:
Removing the door card is easy. 5 mins
-> removing the door glass is a pain, just take your time and use angles to get the glass out - Patience
And stick the plastic back down when your done. Prevents dust and importantly wind noise....