I have downloaded a map that does not overlap (real colors) (not possible to get overlapping due to many reasons). To fill in the spaces between the maps (black) i have created two (purple and red, for illustrativ purposes here on the forum) off set maps. (The complete map will consist of 180 images).
The maps where initially PDF and i used https://pdfresizer.com/convert to crop and convert the pdf to PNG.
When i use photomerg, Reposition, i get bad lineups on several of the merges.
How can i get perfect linup?
When you are aligning image manually. You need to use image that can be aligned perfectly. It looks like the image you are using can not be aligned perfectly. So you will need to fudge the miss alignment make selections you dupe to a new layer and distort the dupe to make it look like they align well. With all the bad alignment you have posted it may not be possible to do that well for it look like all the images you use are not scaled the same there are many size problems it not just an alignment problem. The content of all 180 image would need common content size. The miss alignment you show is not consistent with a common image content scale