I tend to surface scratch my mods also. It is pretty hard not too unless you wear white gloves and place your mod on a fluffy silk pillow stuffed with unicorn pelt.
I really like not to think of these as display models that sit on a shelf for no one to see or enjoy. They are for use and enjoyment and character makes it "your own".
A nice polish every 3-6 months seems to be my routine and I am a big fan of Autosol products.
Metal Care
Their polish is the best and removes surface scratches beautifully. I would recommend as many, the metal polish, a soft rag and just a little bit of time and you will be impressed.