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Interesting video - pretty dramatic changes to the landscape. I've been working on an online service for aerial video processing - the main idea is stabilizing video to erase wiggles, sharp movements, that kind of thing. Tony, I grabbed one of your clips and ran it through the stabilizer...

You could try dedicated panorama stitching software - http://hugin.sourceforge.net/ is solid. Normally for panoramas you try to pivot the camera about its optical center, so I don't know how it would work with such a large translation. You might find luck with trying different projection modes.