First, the ghost images: If the clear scenery tool doesn't work (normally doesn't), then try building the exact same thing on that spot- same angle and everything. Then delete that and hopefully it'll take the ghost stuff with it. If that doesn't work, then I'm afraid you're stuck.
Now to the mine train...
I'm glad that you want to build the mountain first. It's the right way to do it... (although it is a lot easier the other way around.) What you need to keep in mind when making the mountain is where do you want the coaster to go and how high at certain points. Try to make the mountains look natural- avoid using the mountain tool in the editor. When building the ride, try to use the long mountainsides as your advatage, using the longest ones for the biggest drops. Use tunnels when you're stuck, but don't overdo it. Try wrapping things around the outside of the mountains and going in and out of valleys and stuff. When all else fails, do it the easy way- coaster first. Just make it look natural... don't pull everything right up to the track.
I'll look for some examples tonight after work.