The following step was inspired by an EEVBlog tutorial on reverse engineering a Rigol DS1054Z. The two photos were then aligned (photoshopped) to fit onto each other when printed. One of the two layers needed to be mirrored, and it took a bit to align all vias. Luckily the two photos was taken with a tripod from the same angle. The result was printed onto plastic photocopy foil.
In some cases traces were hidden under chips or other parts. I used my multimeter (set to measuring resistance) and needle pin tips to trace them: