Two or three years ago the New Yorker ran an article about digitizing a large tapestry. As I remember the tapestry was laid out on a floor, and a high-resolution scanner was moved over it on a framework of some sort.
This took a while (days or weeks) and the fabric, responding to changes in temperature and moisture, would slightly moved between the times when different sections were digitized. Reconstructing the original appearance of the tapestry in the digitization became quite a problem
This seems to resemble your problem in several aspects.
The article describes how two mathematicians solved the problem.
Though it concentrated more on the human side of the issue than the technical, it still contained a few hints as to how they did it.
I'd suggest reading that article to see what you can glean. At the very least it can provide with some names to use either for a literature search or to contact directly.
A hint is that the tapestry featured a unicorn, and that word was probably in the title of the article.
If you have trouble locating it, try writing me.