The Z-axis homing problem could be solved by adding a "pause" command (gcode M0, I reckon) at the very start.
The printer calibrates, pauses, you attach the pen, press continue, and it'll do the plot without zeroing the Z-axis again.
So does this mean if you give it a swivel knife it can also be a vinyl cutter?
Very nice! I used the same trick to make a PCB by making the printer use a marker to draw on the parts that I didn't want to etch:
Not a 3D printer but really cool video by Stuff Made Here explaining how he tried to make 'realistic' handwritten forgeries with a pen plotter: https://www.youtube.com/watch?v=cQO2XTP7QDw