I now have a couple of years and dozens of successful boards cut on my 6040 router - and some bad ones too.
Boards are all cut from 2 1/2 x 4 inch single side pcb stock. I made a jig for drilling holes in the corners to secure them to the fixture I made for the router with nylon 8-32 socket head cap screws. They're nylon so I won't ruin a bit if I screw up.
The fixture is a block of HDPE which has four recessed 10-32 socket head cap screws in the corners with Tee-nuts to hold it down against the router bed. I've found that it is never really level as I put it down, and so I take a leveling pass with a fly cutter and then it is level. I have a leveling G-Code snippet for the block which takes off .005. I run all of this on LinuxCNC.
I started cutting with the 15 Degree etcher which came with the router. It worked very well after I got sharper on how to set it's height. Then I bought additional bits, but none of them worked as well as the original until I bought a 15 degree 3 flute tapered stub EM3E8-0100-15V from Precise Bits. It does beautiful work requiring very little "adjusting" It is wonderful.
I've had no problems with pcbgcode - worked out of the box.
My designs have all traces on bottom of card and so far no vias.
I export the Eagle design to DXF and use AutoCad to lay out the physical board, rounded (filleted) corners, mounting holes in corners, then run dxf of the board through SheetCAM to get G-code for the outline and corner hole milling.
Typically my projects have a microcontroller (Teensy 3.2) 28 pin DIL and a number of sensors, switches, maybe an OLED, a buck-type power supply and some Molex connectors for remote devices.
My problem is that Eagle doesn't seem to be able to autoroute traces among the pins on the devices without shorts - in other words it doesn't follow its clearance rules. The result is that I have to go through the Board, find where traces are too close to each other or too close to pads and move them, often using the Alt key because they lock to a grid which seems to be part of problem. This doesn't take long, but it seems to me that Eagle should get it right without any help.
I'm using only library components, trace width of 10 mill and clearance of 14 mill. Since the bit is 10 mil, maybe I should be using 10 mill as the clearance rule?
If you guys aren't having to do all this editing, where do you think I'm messing up?