Machined the rest of the 00003-001 on the 00001 CNC prototype. Learned a lot about offsets and the controller. Some lessons learned about the FreeCAD CAM toolbox include oversizing the stock, even in XY if that does not represent the actual material, as this will allow you to be slightly off in zeroing the part, which will save time, since the edge finder takes forever to use. To remove collets from the spindle, after unscrewing, you can choke the collet with one of the wrenches and jam the other one in the gap between it and the spindle and twist, and any stuck collet will pop right off.
Used the CNC as a manual mill by jogging directly and inputting specific MDI Gcode commands to face certain areas and trim the long direction to size. Also use a tiny center drill on the CNC to precisely position all the holes, though I did drill manually on the drill press and tap by hand.
All in all, took a few hours to make this part, but a lot of that was the learning curve. The other parts are basically copies with some minor simplifications, so I will be sure to time how long those take to produce.