I have used Corel Photopaint for stitching both photos and scanned images. Panoramas one image high are easy but I have also done matrices of up to 6 images in a 2 by 3 grid with a fair amount of success.
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no 2 scanner passes are ever truly identical with respect to brightness and color
First of all, there should be a reasonable overlap in the two images to be joined, so that you can taper the edge of one from fully opaque to fully transparent. With scanned images, the joint should then have no noticeable difference in colour or brightness.
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Getting the angles just right can be very time consuming.
With Photopaint, correcting this is quite easy. (Paint or Photoshop is probable very similar.
1. Position the upper image (the one with the transparent edge) over the lower image such that a single distinguishing feature merge together. In your case, Rod, this could be a dot showing the location of a town.
2. Move the point around which one of the images rotates so that it is directly over this feature.
3. Rotate that image until it matches the other image as seen though the transparent section.
I find this process works best if you take the image feature in step one at one end of the join and then rotate one image to match up points at the other end of the join.
(If you are working from photos rather than scans, you may also need to adjust the size of one image.)