I come to this website and check the mod forum just to find a mod like this. I can't really help you with any of these things unless you need textures or something.

From what I can tell scaling planets is really hard. Someone found a way to scale them up in XSi then pull them back into the game (making them larger) but the cloud layer wouldn't scale with it.

The Last Stand, the mod I am working on, aims among other things to resize planets, stars and gravity wells, not to completely realistic scale (because that would make the game completely unplayable for anyone who likes to see their ships cross a sector in less than a couple of days), but to such an extent which impart a sense of realism visually. So the planets are going to dominate a gravity well, gravity wells of stars are going to be comparatively large etc.

(that "someone" was probably me unless someone else also griped about the cloud layer, but lately I found some new interesting files and it may be possible to actually get the cloud layer to work after all)

I doubt anything can be done with orbiting though. Right now there is no way to alter ship pathing and behaviour.