Marc and list,
I found that when you go into the route editor to fix the ground covering the tracks, you need to work from the top of the hill down towards the bottom. What I did was start at the top of the grade, selected the track section and pressed the <ctrl>+Y buttons to lower the ground below track level, deselect that section and select the next section downgrade until all track was above ground level. This worked quite well. I even fixed the DM&IR mains to make them look better. The only thing I don't like about the route editor is when you are changing grades around an overpass, 70 degrees is the steepest setting you seem to be able to use.

There are places were this is not enough of a grade and what happens is the roads and / or tracks running under a bridge become covered with ground. So you either end up with ground covering the road or tracks below or have tracks floating on air just before they land on the bridge. All in all I guess it's not too bad for version 1 of MSTS. I just hope that when MSTS comes out with version 2, we will still be able to use the LTV / Erie Mining route.
Rich S.