A little more on the background story, flashback and all. Don't worry, I promise it will make sense in the end. Kind of :).
Technicalities: I discovered, thanks to some random stranger in the internets, that it's better to forget about extracting ink via transparent images the way I was doing it, and using Multiply plus level calibration to remove the paper texture and the pencils instead. It's worth mentioning that these days I don't even erase the pencil before scanning, it goes away magically, for such is the miracle of computing. So you just take a scanned image, alter the color levels to make a smooth white background and put the resulting image into its own layer on top of all other layers, with a filter of Multiply. It works wonderfully.