My approach has been to install the waterboards, then the top wale level with the waterboards...sand and finish that, then a bulwark wale with the scuppers cut into the bottom edge. The kit planking plan (below) shows the quarterdeck step is managed by just stopping a plank at the great beam and the next plank running straight through. The problem is that you cant just do this because the foredeck waterway and the quarterdeck waterway are not a plank different in height...they are only about half a plank My solution (lucky) was to use some spare stock half the plank width for the quarterdeck top wale...that way you can get the wales level with their waterways and also run the longer plank straight through. You could also cut down a plank to half width if you had to. Maybe this is reflecting an earlier mistake but I dont think so as the deck planking levels are right.
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