What I do currently is put the board together including pots, install it with knobs, place tape underneath the knobs to form my margins, and take it all back apart
That's pretty much how I used to do it, except I was just mounting loose pots to hold the knobs.
Another faster way to temporarily use knobs would be to get some 1/4" rod, cut it into small pieces, and mount your knobs to the rod stubs. That way you could place and remove the knobs through the top side without having to mount anything. (similar to what I'm doing with the brass dummy knobs)
So you write a word down on another pedal and that's how you know the length of the word, measure it with the calipers and you're able to reference the left side caliper blade on your stencil to locate the beginning of the word?
There are a couple enclosures that sit on the table to support the ruler and template at the same height as the one getting lettered. I've got masking tape on those for writing out my test words. I don't have to pre-write every word since a lot of pedals use the same couple.
Once I have the word width set on the caliper, I set the caliper jaws against the brass knob, visually square the caliper to the enclosure, and rotate the knob until an ink mark on the knob lines up with the left edge. Then when I take the caliper away, the ink mark indicates my starting point. It works as long as the word is narrower than the knob I'm going to use.
Have you considered how difficult it would be to machine your own stencils
If I had a cnc router/ engraver that would be a cool project. All my machines are manual though.
Bouncing between letters on the alphabet template isn't that bad once you get used to it.
once you engineer the process, following thru with the work is less stressful
I do enjoy doing it once it's all set up. I've only been doing it once a year though, and just lettering a big batch of enclosures for whatever pcbs I bought that year. The last batch turned out to be a lot bigger than my winter building motivation, so I've still got most of them waiting to get built out.