Is there a preferred way to adjust the brass runners in the scabbard throat so that the dagger slides in smoothly and doesn't get sratched by the brass?

Not without removing the runners from the scabbard which provides a great opportunity to damage something. That top fitting usually cannot be removed without prying. Once you get it out you can bend the runners outward but that may have little effect because they will be squeezed together by the scabbard shell when you reinsert it. You are better off using a flat piece of metal or wood covered with a soft cloth to clean the runners without removimg them. Even just a flat piece of balsa or other soft wood might work.

Might be best to just leave the blade out of the scabbard.

"Might be best to just leave the blade out of the scabbard."

That's just what I've done so far,

I agree leave the blades out of the scabbards.