PCB Alignment for double-sided milling

I wanted to be able to mill the top, flip the board, mill the bottom, drill the bottom, all without having to re-set the X and Y home position.

First off, I use the non-commercial CADsoft Eagle license, which limits me to a 3x4" board.  I decided to use board mounting holes to do "double duty" - mounting holes and  aligning the boards for milling.  I pre-drilled a bunch of PCB 'raw stock' with two precisely placed mounting holes (more on that later).

Alignment pins need to be placed on the top side of the sacrificial board.  To do this, mount the X-Y home block and home the X & Y axis.  Then drill four 0.125" holes 0.3" deep into the top of the sacrificial board at:

1. X =  3.80, Y = 0.15
2. X =  0.15, Y = 0.15
3. X = -0.15, Y = 0.15
4. X = -3.80, Y = 0.15

I cut-off some old, broken drill bit shanks to 0.4", chamfered the ends a bit to ensure no burs and epoxied them into the holes.

Sacrificial board, top view.
(click for larger image)

The image shows the sacrificial board, mounted on the milling table.  I could extend the life by drilling half of my boards via the top, and half via the bottom.  In the image, you can see all the drilling so far is via the bottom of the board.  No particular reason.

PCB mounts to the left two pins (negative X coordinates) for bottom etching/drilling and flips over to the right two pins (positive X coordinates) for top etching/drilling.  Thin double-sided tape is used to hold the PCB securely to the sacrificial board.