New answers tagged image-stitching
Although it would reduce the quality a little, you might try exporting the results of your first example using the highest quality compression settings available and then stitching the last photo to your saved image. If you could save the first effort as a 16-bit tiff, for example, you would lose very little in terms of image quality.
I do not know AutoPano, but are you able to mask parts of photos you do not want to use and/or force to use other parts?
Hugin can do this. The only tricky part is that you need to choose the correct optimizer setting ("positions and translation") to tell Hugin that your camera has moved between shots. Here are a couple of tutorials for using Hugin like this: Stitching murals using mosaic mode by Terry Duell Stitching flat scanned images by Bruno Postle Linear Panoramas ...
Microsoft ICE (Image Composite Editor) is free (can be downloaded from here) and can perform the task you describe (and many more).
IMO, using Photoshop to manually stitch several photos together is probably going to be the most accurate, precise way of achieving this. Automatic photo stitchers aren't anywhere close to perfect, and though it will take a ton of time, manual Photoshopping is probably the best choice. Especially if the end result is for a professional sale.
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