Thought I would post an update. It’s done now and I REALLY appreciate all of the help.
A few lessons learned for the benefit of future readers:
The parallax and optical distortions you get from trying to photograph something like this make the accurate tracing method almost impossible. I even tried taping my crosshairs on the backside to reduce reflections, which helped only a little. I more or less ended up using calipers to make accurate measurements and drawing it in Linearity Curve from those measurements. This pic is one of many I tried with and without flash, playing with lighting, etc.
The edge jig did work, and the first cut into the cardboard was a great idea for whoever originated that one! Next pic shows some of the jig. I used very strong magnets to hold my 2x4 in place. If you look in the pic above, you can also see some weaker magnets that I used to hold the height fixtures in place. They are the dark gray donuts inside the basswood donuts. All of that was cut from 1/4” basswood off Amazon.
WRT to focusing, I was torn on this. On the one hand, I believe there is enough error inherent in height with either a tape target (which you can see above) or the wet paper towel to cool the glass during engraving (which is what I used for a target after the first one) that I think you might lose a little laser power. On the other hand, the app is going to make you re-focus anyway, as noted above. I may go back an try it with a caliper for the next proof piece that I make. I could not detect any difference between engravings done with initial focus on the masking tape and initial focus on the surface of the carefully smoothed out (to get out air bubbles) wet paper towel.
Speaking of wet, I made the mistake of squeezing out the water from the paper towel the first time I did this. The paper towel dried out completely in places, and I am probably lucky I didn’t crack the glass or set the paper towel on fire. The rest of them were soaking wet and dripping, and none of them dried out like the first one.
My settings were on the hot side to get a good engrave, and I think part of that is that the laser is not focussed right on the surface, but rather a few thou above it. I did do a couple of proofs at higher speeds, one of which was clearly too light, and the next one was almost there. The settings that follow were my third run. There were two company logos involved, one of which has some very fine lines that didn’t want to show up well, and that one was done at 700/full/340 LPI. The text was done at 725/full/340, and the other company logo, which was much “denser” was done at 750/full/340. Overall, the engraving came out well and I think all four companies receiving these (one of which is mine) will be happy.