I agree 100% that some sort of "pause and save" function would be really great. I hope they implement it someday - but for what it's worth people have been asking for that since the beginning, and I sense it's not too high on the list of priorities. This is pure speculation on my part, though!
It might be worth your time to learn to do this manually by editing the g-code. It's annoying, but in a case like the 11 hours of air-cutting you describe, it's probably worth it. I have a VERY primitive understanding of g-code, so I'm sure there's easier ways to do this, but in your case what you might have done is:
1. open the g-code file in a simulator - CAMotics is the one I use but I'm sure there are better - and scrub through the visual simulation of the cutting program until you find where it stopped
2. note the line number, which CAMotics shows you
3. open the g-code file in a text editor - I use Text Wrangler - and locate that line number
4. go backwards from there until you find the previous time the spindle is being moved to your z-clearance height. It will look like this:
G0Z12.000 with 12.000 being replaced by whatever z-clearance you set.
5. select the line right before that one, and then select all the way back to the start of the document, stopping before you get to this bit:
Note that your M3 S9000 line will likely have a different spindle speed. Also your header might look different, since I'm using a Nomad. Perhaps a Shapeoko user will post what the correct header looks like.
- Now delete everything you selected.
- Save as a new document and, very important, run it through your simulator again to make sure it seems correct.
- You should be able to now run this g-code and not have to sit for 11 hours while your machine cuts air.
I do this all the time on my Nomad, and it works perfectly. I'm pretty sure it should work for a Shapeoko, but I can't be 100%. Hopefully someone can verify.
Also, if there's interest, I can make a quick video walkthrough of how to do this process, plus how to use calipers to achieve the same thing, though it's a bit harder, but not much.