1200 PPI may be overkill, but you might as well scan them that high for the purpose of archiving them. I wouldn't suggest using such a high res file for creating digital paintings or composites, though, as the file sizes would be ginormous. I create all of mine at 300 PPI and it's more than enough. I believe FAA prints at half that resolution.
As far as the blue tint goes, it's because paper is not pure white, it usually has a hue that can come out during scanning. Same goes with the graphite and charcoal. If it is affecting your piece, just desaturate the layer or run it through the black & white function before you start on your composite. If I want bolder pencil lines in my work, I'll even run it through the threshold function, which automatically turns it true black and white (no shades of gray even).
If you are not already, really familiarize yourself with the selection tools and layer masks, and invest some time in finding some nice PS pencil and charcoal brushes that you can use to mimic the line styles of your pieces to fill in minor gaps so you don't have to clone so much. Also, steer clear of the smudge tool for things like this. It makes those sections blurry at 100% and pretty much defeats the purpose.
Good luck!