In the spirit of trying to think ahead I dry-fitted the two upper decks to make sure they lined up as expected. Of course they did not. The two outer stern counter pieces, despite fitting snugly to the rear-most bulkhead frame, did not slant inward enough to support the aft-most end of the quarterdeck.
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Prizing the already-glued counter pieces from the frame was a bit of a concern, but a single-edged razor blade took care of that job quite well. I could then apply a deeper angle to the host slot on the frame, as well as a bevel the inner vertical edges of the counter pieces to effect a flush fit against the bulkhead.
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The outer stern counter pieces now line up accurately with the rear edges of the quarterdeck, although I will refrain from glueing them in place just yet in case something else unexpected turns up
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