From all the threads I've looked at, it seems that you have got all the greatest hits of "how not to build a layout".  I have to wonder whether you have plumbed the useful articles found in the mainstream Model Railway mags.  BRM, Model Rail and Hornby Mag frequently have pieces on layout building.

Fortunately, I think you have started in the right way by building something small and are now learning lessons.  You probably want to assess whether the layout you have suits you or whether you might want to try again with something new.

John

What you have done should be recoverable and improved.  Try scraping all the ballast off the top of the sleepers (small screwdriver) and filling in any areas where ballast is thin or missing.  Once dry apply a thickish wash of dark brown paint (enamel or acrylic - I only use the latter) all over the ballast, sleepers and rail sides, wipe the top of the rail as you go, including the inner edge of the rail top for good electrical pick-up.  Have a look at photos of ballasted old rail, sleepers and ballast tend to be all roughly the same colour.  Don't be tempted to pick-out the rail sides in bright rust colour - this will look awful!