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.
--Wayne