As discussed in previous installments, it's best practices to scan detailed art materials that will be reproduced at-size (photo negatives, print scans) at 1200 ppi (the exception being documents solely with text, which you can often get away with scanning at 600 ppi and upscaling later, to save scan time). And I generally scan original artwork (which was drawn at a much larger size than the finished book) at 600 ppi.
I'd also recommend always scanning in COLOR versus grayscale, even though the files will end up lineart/1-bit images. Why? A color scan takes the same amount of time as a grayscale scan—the grayscale scan is just the scanner scanning in color as normal and arbitrarily throwing out two of the color channels. Scanning in color gives you maximum flexibility for how this grayscale conversion happens, and that conversion can happen as part of your script/"Action". Have a red ink spill on your artwork? Use blue-line pencil under your inks? These are easy to eliminate from a color scan and could require some serious work from a grayscale scan. (For one page of the Cerebus restoration project, I actually eliminated an entire watercolor-painted overlay to a page of original artwork with the Photoshop "Black and White" tool, taking a page that would otherwise have been completely unusable and looked perfect afterwards. This was only possible because of the color scan).
Plus, you might find use for your color scans in the future. Art books? Promotional materials? Crazy enlargements on the side of a building? You never know when you might want to return to the source, and that piece of artwork might not always be as accessible as it is right now.
When we get to negatives, we'll discuss bit depth again, but for your original destined-to-be-line-art artwork, 24-bit depth (i.e. 8 bits of depth for each of the three color channels) is more than adequate.
(Also—this won't be a problem if you're using Vuescan, but I want to reiterate it anyway—DON'T SHARPEN YOUR IMAGE while you're scanning! Is there an "Unsharp Mask" box somewhere? Uncheck it. We will do sharpening at the next stage, in a controlled way, AFTER we've upscaled, to avoid any possible negative effects. (This is one of those things that can be totally fine, depending on a whole host of things—but best to do it in a purposeful way rather than whatever arbitrary radius etc the scanning program wants to apply.)
The Epson 10000XL/11000XL/12000XL, which is the scanner used by everyone scanning original artwork for the Cerebus restoration project, has an oddity that needs to be taken into account— it has a variable focus to accommodate scanning artwork that can't be flush to the glass. Because of this, you need to make sure it's in focus before starting a big batch of scans. Hitting Control-F in Vuescan should cause the focus to adjust. If Vuescan crashes and defaults to the standard settings, you'll need to focus again.