So I made a 3d model from 21 pictures with 123dcatch, I removed the unnecessary parts with blender. Then I merged the 2 4096x4096 texture with a python script.
But now I have a 8096x8096 file with half of the space being empty and certain part not being used

for example I want to remove what I circled in red and move what I circled in blue at it's place. I also want to crop the texture file.
Is that possible?