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The last time I used graph paper to lay out a board for etching and drilling was early 1990s, before I had a PC. Nowadays I would print out a 1:1 scale guide and center-punch it. Another possibility, if the entire board were laid out on a 0.100" grid, would be to make a sandwich with printed guide on top, perfboard in middle, and etched board on bottom. Get them lined up and fastened together, and you don't need a center punch; the perfboard ensures that the bit doesn't wander. If you're making a small run of identical boards, carefully drill the first one using either of those methods, then use the first one as a guide to drill the others. You could even stack a few and drill them all together.Maybe find something somewhere with holes already drilled, then use that as a guide.
Small holes would be best then you can enlarge them later.
I had to do a few patterns in the past myself but what i did was used graph paper taped to the board to be drilled and a very very sharp center punch to mark the center of each hole. It's a very very difficult and tedious process to do it that way however, suitable only for a one-off project.