My laser set-up isn’t on an MPCNC (yet…) and doesn’t even have a Z-axis. I adjust my Z with a couple of set screws before each burn. The distance where the beam focuses at it’s smallest point will vary depending on which lens you have but my point is that this distance is fixed and once you know what that distance is you can create a “gauge” to quickly set the laser from the work surface by that same amount of distance each and every time. That way you can set your Z laser distance from the work surface without even turning the laser on. When I set my laser I just loosen the set screws and drop the laser heatsink onto my “gauge”. Then I just tighten the set screws and I’m done.
As far as finding that perfect focus distance goes, I think the Jtech site makes a good suggestion about turning the beam power really low. I also found that a matte black or gray surface is best for focusing the spot size. It’s hard to tell how small the spot is on a bright or reflective surface. If the power is really low, like M106 S10 or S5, you can take the laser goggles off and look at it directly without frying your retina. Very hard to see the laser at low power with the goggles on.
The order you choose is up to you. You can set the focus, measure it and then create a gauge to match or you can work backwards. Create the gage and try to get the focus distance set tp the same as the gage by using the fine adjustment on the lens cap. I went the second route because all I had was a ruler and it was hard to measure a straight distance with obstacles in my way.