I have done all of my splicing of flatbed scans with a program packaged by Canon with its digital cameras, called Photostitch. It has a setting for splicing flatbed scans. My experience is that if I use the same exposure on all the scans, the software gives a seamless final product, no adjustments needed. The software handles the alignment automatically.
As an FYI, although Photostitch has been great (perfect, really) at stitching flatbed scans, I thinks there are better programs for creating panoramas from conventional photos. For example, I experimented with PT Assembler (www.tawbaware.com
), and got an excellent result.
If you can't get your hands on Photostitch, you might try searching for another panorama program that handles flatbed scans.