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Hi Colin,
I have two suggestions which you may have already considered. Sequence Generator Pro has an awesome Mozaic wizard for creating the sequence. It would work very well for what you are proposing.
As for the processing, Pixinsight has some really good tools such as mozaic by coordinates for registering the files and Gradient merge mosaic for integrating them. I use both these tools quite often and work really well. Hope you go ahead with it, sounds like an amazing project.
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