[raynor]

All of your resource production, intel points and research points are added straight into your score. Your number of planets and population affect the score indirectly through their affect on increased production.

In older Versions of the game, your mothballed ships affected your score. Under the new Version, this is no longer the case. So, you could mothball your ships instead of scrapping them.

SJ's advice is very good. Pump all your excess resources into units--fighters in particular. In the early game, I think you are far better off building fighters than building storage for your excess minerals.