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Sure, I can do it manually with photoshop, but it's a hell of a lot of work. If there is something that will do a lot of it automatically that would help.

Automatic panorama-stitching software does tend to assume that all the shots are taken from roughly the same point. 2D aerial photograph stitching, where you're not at exactly the same height the whole time, and you only get 20% overlap (enough to see both sides of a vertical object in the overlap area), is a much harder problem and I don't think you'll find a faster solution than using manual stitching (and you'll need a good manual stitching program that allows arbitrary 2D transformations between frames). Even Videorbits only does 1D stitching (you can make a linear panorama but not a tiled one) and to do it automatically it needs ~95% overlap.

Peter