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OK Geoff. So if you've got the luminance stitched ok, you're nearly there. Registar is not logical at times. Given where you are at, why not use the luminance as the reference for the colour data?
Under the Registar Groups Manager window, purge everything from the active groups, this will place them into the archived groups - delete them from there as well. Make sure there's no reference groups in either.
Open up the luminance that you've stitch together. If this is still in PSD format or similar, flatten it before hand. With the luminance open, locate the stars (if this hasn't already been done before). Then open up the colour data that you will register against the luminance (reference image). Start registering each colour panel against the luminance.
When done, save each of the registered colour panels, then open them up in photoshop. Stretch and stitch them together. They'll align perfectly assuming your luminance is a good match. With the colour panels stitched you can introduce the luminance. The colour and luminance will align to produce and LRGB style image.
Hope this makes sense. Don't try to re-register against existing registration groups. You're bound to end up in trouble. Clear them out before doing the above.
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