Paul,
I brought home one of those scanners with the film scanner gizmos and only had it a day before I exchanged it, but I cut a piece of posterboard the same size as the scanner lid and taped it onto the inside of the lid. That way you can make your scan background black, or white or something else if you prefer.
As far as scanning goes, does your scanner software let you preview the scan and then choose the area that it actually scans? Some of these scanners will automatically balance the color and brightness once you narrow down the area you want to scan. I don't know if this will remove the colored horizontal stripes you're getting on your Rail City card, though.