What file format are you scanning/saving to? BMP or somthing 'uncompressed, i.e. NOT .jpg ???
For clarity i go with .BMP at the expense of LARGE files.
Also try reducing the colour-palette in your final pix, since the BGlass artwork aren't photo-quality (millions of colours) and something similar to cartoon quality, you could reduce your colour palette from 64million colours down to 256 colours with no image degradation.
This would reduce a LARGE file into a relatively small(er) file to worjk with, especially if you have RAM limitations.
Reducing the colour palette may also help reproduce the exact colours on your BackGlass.
If you scanned a uniform yellow area on the BG, you dont wan't to be working with 100's or 1000's of shades of 'that yellow' in your final scan.
food for thought
MM.