This is a fun demo but, as others have mentioned, simulated annealing really isn't necessary, or even that appropriate, for this specific problem. I threw together the same demo with a very trivial algorithm that I think does a more accurate job of reconstructing the same images in significantly less time than the simulated annealing [1]. The algorithm consists of first finding the closest matching pair of pixels as a seed. It then finds the remaining column that most closely matches one of the current edges and adds it to the reconstructed columns. This then repeats until there are no remaining columns.
On a different note, if this quote:
> The unscrambling problem being solved here is much harder than a typical unscrambling problem, because we are rearranging single columns of pixels.
is referring to reconstructing shredded strips of paper then it is laughably false. The single columns of pixels are extremely clean and correspond very, very closely to their neighboring columns. In reality, the tearing of the paper makes the edges not match very well and it's just much noisier in general. I've worked on this problem before and it's many orders of magnitude more challenging than the reconstruction that is done in this demo.
[1] http://sangaline.com/blog/image_unshredder/