It performs matches of the 'maximumly distributed high entropy points' until it find 3 good matches that results in the same offset, The maps are merged, and then the script proceeds to the next image to find more overlaps.
If it find 3 matches at 3 different location, it decides no good overlap can be found at this time and aborts to next image. But it currently does not cycle back to this image later when later image overlaps are found.
One small speed improvement would be to select the next search around where a 'good' match was found, but as it stands it is ensuring it isn't getting a false possible by doing a lot of failed searches away from the 'good' point before trying another one near the good point.
My initial guess at 9x9 (radius 4) was good. The search times was not excessive from base level, and rarely does it find a false positive match (let alone 3 different 'bad' matches). Smaller sub-images and you start getting too many false positives, to the detriment to finding a correct match, larger and it gets slower though not overly so.
Perhaps sizing the sub-image, based on distance between the search point and other search points looked at (and edges), would work better. when search areas get too small the overlap seems less likely to even exist.
In any case I am now very happy with the script and the results it generates. In fact I re-produced my current large map from all the small ones in quite a short amount of time, with little in the way of hand on involvement. I just set to to go and come back later.
Current script is
http://www.imagemagick.org/Usage/scripts/overlap
Next item would be to have the script loop back over 'failed overlap' images, if it reaches the end of the input image list and it had found some new overlap that was added to the main image. That way even if a image fails to match, it may match after some other image was added (overlap of a recently added overlapping image). That would make it even more automated, so I can just set up and let it work in background.
FYI... here is a map that was pieced together using this program.
