To hide things from your players, I would consider putting things on different layers, then you can reveal one layer at a time as they explore the area. You'll have to predetermine which chunks to reveal of course, but this is a good idea revealing things piece by piece.

For elevation, as JimP suggested, contours are the best. Since you are using Mike Schely Overland, there is a contour tool called Height Contour in the :CC2MI: catalog. It looks white int he preview, but it is transparent, and you can lay multiple on top of each other to lighten it bit by bit.

I don't see any reason why they have to be 10' wide, unless they at some time had to be widened to that point to bring large objects through. In the real world, quite a lot of underground passages are narrow things, not even 5'.

You'll need to contact support by email, and they'll help you out.

Once you've entered this command, it is the new default until you set a new value, it is not a per-map setting. And it is a good setting for everyone to use unless you have an old computer with very little memory (below 8 gigs)

No, trace won't work on entities on frozen layers