I also prepared a video last week of the whole process.
Now, on to how these problems were solved, in order of simplicity.
5) Drifting Hole
This was easily fixed by enabling the tapping feature of pcb-gcode.
2) Bad Motor Coupling
Here is an exaggerated image of the problem I was dealing with.
3) Not Round
4) Incomplete / Grounded Pad
6) Inconsistent Traces
All of these problems can be attributed to the part that connects the y axis threaded rod to the bed.
1) PCB Thickness Tolerance
I am releasing the beta software I am using to add probing routines to the gcode produced through pcb-gcode. I'm calling it PcbSubtraction. I hope to extend it and add more documentation over time.