3000 and 5000? does that even exist? never heard about that. the finer grade i ever seen was 2500, and it was extremely smooth.
higher than that you usually go for a polishing paste ... i guess autopolish is one of the known brands, but i guess there must be better products out there too.
as for the clear coat ... be careful. the clear coat may not be that thick, specially if the paint is a bit old. And you may end up going through it into the paint in some places like borders or bumps.
if the scratch is really thin, yeah a nice polish should do the trick.