I guess they are too small, If I will scale them up individually on the UV map it should solve it?
It should! The larger they are on the UV map, the more pixels they’ll have to work with.
Now, another problem during baking is that the first bake took 10 min, the bake for the second part (without clearing the image) took 1 hour, the third part more then 5 hours, I had to stop it in the middle, and I am only half way there, am I doing something wrong?
Shoot, it sounds like this bug is still a big issue!
⚓ T60428 Using subdiv modifier affects normal baking performance of all objects in scene (blender.org)
You can chime in on that thread if you’d like to hopefully bring more attention to this bug, or read through it for more information. I really thought it would have been fixed by now!