Took another crack at trying to drill through holes with the mini CNC. Short story, still doesn't work but I figured out why the origin/home is so far away, at least when using KiCAD.
I would be nice to upgrade the CNC to use a Smoothie Board, doing away with the need to use Real-Time Linux, not sure if the owner would be keen, but at $45 I feel it would be a worthy investment.