...and crap, it's fun and rewarding (it looks so much better without the SFX!!). Scanlating this is gonna take twice as long now.
The workflow right now for cleaning is really tedious right now though.
First, I open the raw in GIMP and use the Clone tool to remove any SFX that are covering art with tone. I can't replicate tone otherwise, so the clone tool is a must. I'll also clone any other patterns over nearby SFX. Any SFX covering large areas of white or black are initially painted over (crudely) in GIMP.
I then save the GIMP file as a regular image, and open the image my go-to art applicaiton, Autodesk Sketchbook. Yeah, I gotta switch apps.
Sketchbook is a must though, because their pencil tools leave lines that look almost exactly like the existing lines. I'm redrawing any art that used to be covered, and having a similar tool makes the redraw look so much more seamless. I haven't figured out yet how to make GIMP tools match that level of quality. However, Sketchbook does not have that essential clone tool, so that has to get done first in GIMP.
Once redrawing is done in Sketchbook, cleaning is usually complete. I go back to GIMP (which happily will open .tiff files; Sketchbook has no idea what .xcf are) and finally go on to do the typesetting. GIMP's text tool is highly superior to that of Sketchbook's, so I use GIMP for this.
Long story short, I don't have any one tool that has all the features I want, so I use a combination to achieve the results I'm looking for. And in the process, complicate my process further :)