Dear Williv, Dear Andy,
I understand that the great number of scanned images from different cameras will make a manual photo-by-photo approach very time consuming and ... boring.
As Nadar mentioned already, Agisoft PS is not well suited for your data, because it is made to process photographic images from which the software is able to calculate / estimate the inner orientation of the camera, utilizing algorithms for camera-self calibration following the concepts of Brown.
Unfortunately the inner orientation will in most cases get lost during the scan-process for reasons I mentioned already. And perhaps there are some more, e.g. the photo was not exactly aligned with the scanner frame etc. etc..
Some time ago I carried out several test-processings with scanned paperprints of WW2 recon images from German Luftwaffe. The drawback with these images was, that the bottom fiducial had been cut off and each scan had another dimension (pixel rows/ columns). On the other hand, I was lucky, because the type of camera, film-dimensions and focallength was known, so that I was able to do a kind of geometric "reconstruction" for each single image. After that procedure some images with sufficient overlap could be aligned, but there were always images that did not.
When you do not need necessarily "orthorectified" images with very precise positioning in your target coordinate system , trying out some kind of image-stitching software my help you out.
But you have to keep in mind, that these kind of software will not necessarily take photgraphic-image distortion into account, which is still inherent in the scans, although it can not be parameterized any more.
Some time ago I tried out Regeemy, which is an automated image stitching package developed by INPE / Brasil, which i found quite good for Satellite images. Please look here:
http://wiki.dpi.inpe.br/doku.php?id=wiki:regeemyGood luck for your project.
kind regards