When the seam goes through the oil pan, I've always scraped, sanded and/or filled the seam. How much work it takes just depends on how good the engine halves match. I always true up the halves on sandpaper laid flat on the table before gluing. I always use plastic cement to help fill the seam with the melted plastic. Sometimes a little putty is needed if there's too much distortion of a large gap.
As for the valleys, it's usually the same deal. More often than not, the valley doesn't show and can take more filing. In other cases, the intake manifold may need some slight truing up with sandpaper of files.
Hope I took this correctly and hit the problem you're talking about.