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Thanks John, separating the RGB channels didn't make much difference. I did realign the RGB channels since I found that the red and blue channels were quite a few pixels off and the realigning did improve the image considerably.
I attempted using WinJupos to de-rotate but the result was actually softer then when I just done a stock standard stack.
All I can do is try and try again... Unless you want to give up your secret in the images you capture in the way of describing your work flow... :-)
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