Thanks @SphaeroX, I have tried trimming them before merging but then sometimes the alignment doesn’t work because of the missing parts, so I do it very little by little.
I’m glad you like the textures! I don’t have tutorials, I’m sorry 
but I can share with you a trick I use, and it’s to open the scan in Zbrush and project the vertex color into a new remeshed lowpoly copy of the scan, and I project it say at a subdivision level 8 (depending on the polycount) and then I go to level 4, and in the places where there’s shinny or shadow or ugly colors, I smooth the color only, then go to level 5 and that has already removed most of the ugliness but the higher details remain, so I smooth the color again (a bit less) in level 5, and again in 6, and so on, until I get to level 8 and the shine or the ugly shadows are gone but there is still a good amount of detail left. This works like a charm! 
I do the same thing with the texture color, and then I export the resulting clean textures and mix them in Photoshop if needed
If I can next time I’ll take screenshots to show you, but I’m not sure I’ll be coming to the forum much more because of some upsetting things that have happened