"He who marches out of step hears another drum." ~ Ken Kesey
I know you know this already but I'll ask anyway, did you convert to spotcolors? One more thing... I've had pencil drawings and the shading looked very good and I really wanted to keep it that way, so I would scan into photoshop add vector text and any other places I wanted a nice clean vector look, but would leave the pencil shade as is and printed that sep all black from cymk turn out very nice. The halftone just didn't look as good and the original pencil shading.
I would normally scan the image and open into Photoshop, RGB or grayscale on this image won't matter much, so go grayscale, it's a smaller file size. Here's an option to try; make a duplicate file (leave the original alone) and convert to Bitmap mode, halftone, and try 40 line at a 22.5° angle, and either elliptical or round dots, OUTPUT RESOLUTION at 1200 ppi, it makes your dots much cleaner). Then you can "Place" it into Illustrator and assign the spot color there. Steve