Had the same issue in Niles Canyon, I ended up making an executive decision and model the terrain a bit, and use the decal more as a guide than the rule. The bottom line was that I was only adjusting grades and the line about 1-3 feet, and when running the train through the canyon it looked the same as in real life (the family rides the canyon a few times a year, and we drive through it every other weekend).
"Just post some random unrelated text. We have members here who can help you with that." ~ Chacal "When all else fails, read the instructions... if that doesn't work either, try following them." ~ Old Prof The Grade Crossing - Atlanta North Project - Virtual Rail Creations
Sadly I don't have the maps for my area. I am having to regrade using averages, or laying the track in the longest sections I can, grade the track so it balances out, and then snap the ground to the track. I tend to use the later approach more.
"Just post some random unrelated text. We have members here who can help you with that." ~ Chacal "When all else fails, read the instructions... if that doesn't work either, try following them." ~ Old Prof The Grade Crossing - Atlanta North Project - Virtual Rail Creations