What size tools and depths of cut did you use?
I used all Dremel bits. To cut the traces, I used a 30 degree engraving bit. The pockets I found the smallest diameter bit I had so I’m not sure what it is. I think it’s a diamond bit, it looks like a gritty metal. It has a slight taper, flat on the bottom. This bit has a 2mm diameter at the bottom.
For engraving: 30 deg V, 5 m/s feed, .3 mm steps and a total depth of .6 mm.
For the pockets, I just needed to remove the coper: 2mm Dia, 5 m/s feed, .3 mm steps and depth of .4mm.
Most of my PC boards are one-off and include a micro-processor like an Arduino, so I make them with perf board, or 3D printed. If your interested, I have several examples here: http://www.instructables.com/id/Custom-Circuit-Boards/
I do a lot of prototyping before I solder, so I’m not to concerned about getting something wrong. I use Fritzing to document my wiring and I also use it to manually route the wiring for my one-off boards. I used Fritzing to do my wiring layout for this project, so I already knew about what it would look like before I made the model.
I will figure out a better software in time, I was just anxious to see if I could get the accuracy to do it. The MPCNC looks like it will do nicely.