If we make an assumption that each board is etched accurately then maybe 2 appropriately placed alignment holes could be drilled [maybe at the diagonal corners of the print], then Tony's visual inspection along with something like a toothpick thru the holes to help align them when they are glued together and finally drill the rest of the holes thru both boards at one time.
Less drilling and possibly better chance of the holes being in the correct place on both sides.
Arvid