I ended up using Estlcam (sorry for my terrible spelling of that everywhere) to lay out the drills, then I saved that gcode. Then I reopened the dxf and layed out the cuts with the downcut bit.
When I ran, I did the drilling first, then I changed the bit and ran the other gcode file.
I’m running them all from the LCD/SD card.
I think using the LCD to move the tool around while I changed out the bit kept my home position. I didn’t push it hard enough to skip any steps, I think.
If I was going to do it again (and I might just start doing this as a general rule) I would turn the spindle on above the origin, and use the LCD to plunge 1mm into the surface at the origin. Pencil marks just aren’t accurate enough. But hopefully I wouldn’t need that.