While I use different software, if I needed both raster and vector elements in a piece I'd go about it like this:
Do the traditional illustration work first, and scan it into the computer at high resolution as stated in your post.
Next, I'd do any raster artwork you need in GIMP. Export the image from GIMP, again, at high resolution.
Import the artwork into Inkscape and do your vector work.
Export the artwork as a PDF from Inkscape, and any vector work you have should remain vector.
I hope this is useful.