If i was doing the job i would also use a jig but slightly different, would make it with 2 holes with an L shape cross section, make all holes on the assembly the same pitch, so you would clamp the jig drill & tap first hole, shouldered bolt goes in that hole, do second hole, move jig down using the shouldered bolt in the second hole drill & tap third hole in so on, the jig can also be used on the clear holes.
For marking out the edge holes - although I've not used one, I've often thought about buying transfer or universal punches in case I needed to transfer holes:
Universal transfer punches or Transfer punch sets:
With the holes drilled in the top surface of one plate you would align it to the edge of the other (using clamps, 90 degree blocks etc.) put the correct punch into the hole and 'transfer' the centre point onto the edge surface.
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