Here's what I do:
- Keep the images in RGB, don't split channels.
- With StarAlignment, produce the first mosaic simply changing reg model to 2-D, activating distortion correction and changing working mode to reg union/mosaic. You can also check frame adapt.
- This will produce a subpar result, ie it will still have the borders quite evident. But this is only an alignment aid to the real thing, so change the name to align and park the image somewhere
- Now, get the mode back to register/match and leave everything else the same. As reference use the parked align image and select the two (I assume is a 2 part mosaic) parts as the images to be aligned. This will produce 2 copies of the aforementioned images, with the same dimensions of the finished mosaic, filled with black area.
- Now take out the splendid GradientMergeMosaic. Simply input the two just aligned images into this tool and make it run. BAM! No more borders.
In the last step, what could go wrong is, if you have a bright enough star on the border of one of the two images, GMM could produce artifacts on the interested border, like a comet thinghy (sorry for the too techincal explanation!). If this happens, go back to the interested aligned image (the one with the big black area in it) and simply cover the star up using clonestamp. Then try again.
I hope I made at least some sense...