First thing is you should never use a machine with discs to remove scratches. All you will do is create many more problems.
To remove scratches you start with a coarser paper like 220 wet, then move to 320, then 400. You should also be using a sanding block to make sure the surface stays flat. You sand the area east to west with 220, then north to south with the 320 then go diagonally with the 400. This way you get the area smooth and flat.
Is this alot of work.................yes........but a paint job is all about the right preparation. You can be the best painter in the world, but if the prep is shoddy the paint will show it right away.