1. The obvious answer is often the best one - yes I can delete the file after verifying the directory. [Edit - now implemented]
2. I don't know if we're at cross-purposes here. All the items that I see on the list are either colours or specific GUI features, such as 'Desktop', 'Window' and 'Menu', each with a little square of colour displaying the system default colour for that feature.
3. The colour in question is pale yellow - RGB code $FFFFD8. The graphs have always been that colour by default (I just happen to like yellow).