The original build never gave incredibly good results, with the bit either not cutting into the copper, or pushing too far through and ripping the board up, not creating viable traces. When it did break the surface, there was a lot of vibration in the tool, causing inconsistent lines. This is shown in the image below:
After some prodding, it seemed that there was a lot of play in the Z axis, due to the shaft coupler having a spring, rather than being completely solid. I had used a coupler like this one:
The resulting board is significantly cleaner, and would actually be functional. I'm excited to mill further circuits, I will update once I have a larger board milled.