That’s why setting the controller for a timed pulse improves the outcome: you get the same pulse energy every time you poke the Pulse button and can tune for best scorch.
That said, I don’t like the look of the pulse at Mirror 1. If I’m seeing it right, there’s a little hole off-center in a ring, which is not the energy distribution of a good tube:
Sacrifice a manila file folder, slash it into little squares with a razor knife, tape 'em to the entrance apertures, find a pulse energy that gives a nice scorch, and let’s test that suspicion.
Also: beam alignment is an iterative process. First you twiddle the grub screws to get the beam parallel to the axes. Then you slide the mirror mounts back-and-forth to center the beam on the mirrors, which wrecks the angular adjustments. So you re-parallelize the beams & tweak the mounts again. Worst case, the machine has an immovable laser head, so you must shim the tube up-or-down to center the beam on M3.
What I went through the last time around turned into a series of posts:
After a while, it becomes meditative …