how about layer registration? If the tolerances are out of whack,
nothing will line up very well.
I think if the individual layers are accurate (or at least equally
distorted), lining up the drilled clad shouldn't be a problem - just
add two corner holes, drill them separately on each board, and pin
them to line up the boards. I think this is an easier problem to
solve than lining up the etch resist on opposite sides of one board.
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