@MrHume, not only can you drill the dowel holes with the Nomad, but if you ever want to do 2-sided machining with MeshCAM you must do so, to accurately re-register the stock when you flip it over.
This is an area where a little hand-written gcode comes in really handy.
I used 1/8" dowel pins becuse they are easily available, and it is convenient to put a 1/8" drill bit right in the collet. Put in the drill bit and move the axes around to where you want the X-Y zero point of your stock to be. Set the drill bit tip down on the spoilboard. Then zero all three axes.
This little program
G20 G90 (inch units, absolute coordinates)
M6 T1 (define the tool as tool 1)
G00 x0.0000 y0.0000 (rapid over to the origin)
G00 Z0.1000 (rapid down to the “safe level”)
F8 (set the feedrate)
M3 S4500 (turn on the spindle at 4500 rpm)
G00 X0.2500 Y-0.0625 (rapid over to the first hole location)
G00 z0.0200 (rapid down to just above the stock)
G01 Z-0.3000 (move down into the stock to drill)
G00 Z0.1000 (rapid up to the safe level)
G00 X-0.0625 Y0.2500 (more of the same as above)
G00 X-0.0625 Y3.2500
G00 Z1.0000 (rapid way up into the air just for the fun of it)
M5 (turn off the spindle)
M30 (end the program)
is what I used to drill the dowel pin holes for my Millennium Falcon attempt. The theory is to offset the holes by the radius of the dowel pin, so when you set the stock up against them, the lower left corner is at X0 Y0. The Z-0.3000 is the depth of the holes, which is not quite all the way through the spoilboard. I used 1/2" long dowel pins so just a little was sticking out. Chamfer the holes before you press in the pins (the MDF will spring back a little and grip the pins tightly) so that the pins don’t bulge up a collar where they enter the surface.
Here is a drawing of the three dowel pins from the sample gcode above, with a representative stock registered against them. This provides a virtual fence along the Y axis and and endstop on the X axis.
When you put the stock down, you just need to re-zero the Z axis using the cutting bit on top of the stock itself. The Nomad will keep track of the X and Y zeros between homings, and in my testing even between power downs, until you re-zero X and Y. The home switches are good to within .001" in my testing, which is well good enough for the belt-driven axes. (Editorial comment–I am very impressed at the level of thought, design, and fabrication that has gone into the Nomad. Every step in the chain is on the equivalent level to every other part, mechanically and electrically)