This is a tough. I have not had any problem with the unify command, but I have not used it on massive sets of lines. It also may be a problem if you are trying to unify non-contiguous lines. The other trouble is even once unified they will still have all the original nodes. I'm not sure if there is any easy way to simplify this.
I usually just trace the contours with splines. It's a bit tedious but even complex sites take only a couple of hours, and that way I have complete control of the outcome. They are also much easier to copy and modify for cut, fill, new and alternate conditions.
