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Having been where you are quite recently I have personally found that the best way is to do the same processing on each frame, doing quite minimal processing premosaicing. I basically set black point, noise reduction and stretch.
After every frame has been "processed" individually, don't worry if the individual ones don't looo crash hot as more processing can be done after they've been stitched together. I have been using Autopano Giga, not cheep but has worked well for me. After it has stitched them together it doesn't look great but after some curves and levels playing it works well.
The first image is a 2x3 panel of the LMC. The second is an 8x10 panel of the galactic centre.
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