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Hi Steve.
I use either ImagesPlus or AstraImage to do my aligning and combining. Its very easy using these. Unfortunately not free though. I found that ImagesPlus does a better job of aligning, and adjusting the colour, but I prefer AstraImage's deconvolution and maximum entropy routines for "sharpening". You could also use Registar for aligning your images, but again it's not free.
You can use Photoshop to align them by layering each final colour channel image and use difference blend to line them up. Just remember to turn the blends back to normal when adding the next layer. Once you have done that you crop the lot to make each layer the same size. You can then combine them using a new document and inserting each layer from the first document into the respective colour channel. I haven't done it so I'm not sure of the exact process.
Don't know how to do it in Registax.
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