The problem will be that the focal point for a flatbed scanner will always be the surface of the glass (this makes sense as otherwise something placed on the glass would be out of focus otherwise!). If you get a scanner where the lid could totally be removed, this might help? You could then hold the scanner up to the object (might need some white paper or cardboard in the background). How small a gap are we talking at the moment - you may be able to find one with a much thinner frame and hence lose less focus.
The other alternative is a handheld scanner with stitching software - some of these were capable of stitching up to A3 size. Don't know if these are still around, but it would make sense that this would be a better solution, as they are designed so that the focal point is where the scanner meets the object being scanned.
