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That's what stable marriage is for. With some reasonable heuristic it should just give you the best partial ordering, which when flattened into a total ordering should give you the most likely picture.

How do you calculate your certainty?

Currently I'm using a matrix to determine adjacency, but I'll give this graph idea a try. Thanks for the tip!

PS. Have you actually realized a succesful implementation? (Just curious)

No problem! Yes, I have this working:

http://webfuel.org/instaunshredderv2.php

It also works on the test images I created:

http://webfuel.org/a.png http://webfuel.org/b.png http://webfuel.org/c.png

This is exactly how I implemented my solution. The worst case scenario is important because some images have last strips that have a unique "next strip" value.