To soften up the face and some other areas, I knockout the black lineart, and add colour instead (on a seperate layer so I can go back if I make a mistake). You''ll probably notice I went out of the lines around the ears; that didn't really matter in this instance because, I was going to put a seperate colour hold layer for the hair on top, and flatten the image before printing, so you wouldn't really see it anyway.
Can i ask you something? When you scan the inks, the inks are mixed with the background. How do you separate the inks from it? Because when i try to lock the pixels, i can't single out the lines and re-color them.
You need to convert the image to bitmap or adjust threshold if you want the image pure black and white. I would strongly suggest cleaning up the image and maybe adjusting levels prior to doing that, so you don't have lots of unwanted drop out, or artefacts on your page..