black areas: burn, brush tools.
white areas: doesn't really effect those I think.
textures: You could replace the texture, preferably taken with the clone stamp tool from a non-messed up part of it on the page, but if not then find that texture somewhere else in the series or internet (it would take a very long time doing it this way). Or a much faster, but not so good looking way, is to just use a low opacity dark color brush and go over it until the general shade of the texture is about the same as the good part of the texture.
lines: line, brush, clone stamp tools. (sometimes line's don't get messed up very much from scan lines, though you're probably asking to do some shonen jump shit scans, so line's will get messed up if they dare stand in the path of a scan line.)
after saying that, I assume you mean scan lines like on this:
http://mangahelpers.com/downloads/read-online/15916/3#apicture
Oh yes and visit
this tutorial for slightly more detailed information