with enough overlap you should be able to get pretty good results from the photomerge feature in photoshop. I've stitched together a four 4x5 negative panorama, and while my imac didn't like it, it was doable. You just need a lot of ram and some patience. With that many frames, you're going to have a massively long image, but the file should be manageable--just make sure you use the identical settings on the scanner and that your exposures are consistent.
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