Rich,
What I did was to take the back board and flip it over on top of the front board with a piece of cardboard in between, attaching them with longer screws, and clamps. Then I ran the program I created, for both the .316 dia though holes and the .496 dia recess at .030 deep. Once the first half was done I flipped everything, aligned it all back up and ran the program on the other half.
Then once completed, I installed all the inserts from the bottom side, insuring they were all just below flush. Then reinstalled them both.
I hope this helps.
