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What software are you using for stacking, Bo? It's a pretty busy field so I guess it's not surprising that it's giving you problems.
Cropping the subs to make them match more closely seems a reasonable approach if all else fails. It would certainly work in PixInsight and differences in size between subs wouldn't matter (by default they would all be registered and cropped/padded to match the reference image.) After cropping I'd probably save them as FITS files before registering them.
Cheers,
Rick.
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