@badskunk and I created a new program and resurfaced the spoil board on the SO3 this morning. While doing so we ended up with a bit of X axis artifacts from the surfacing bit however overall it’s an improvement and now we know we likely need to re-tram the spindle.
Reminder: If you are going to be cutting through your material you must use your own spoil/sacrificial board when doing so.
Sweet! Thanks, Jay! I’ll be stopping by this evening and will be sure to mess it all up for you! 
I’ve started using the Shapeoko to mill out plastic soft jaws for holding some of my less “orthogonally friendly” aluminum projects in the Bridgeport vise, and it’s worked great so far! Thanks again for teaching, it’s a very helpful tool to have! 
The router has been trammed and the spoil board has been resurfaced again.
