Thanks, Cat. The transom fits as the quarter panels are attached now, and the bottom presumably fits since the tops of all panels fit together at the top as prescribed, but I have realigned my quarters a bit. The top edge now aligns with the #4 panel, inside corner to inside corner, like the other panel edges. The bottom still aligns with the flat as pictured above, so it’s far from inside corner to inside corner with the #4 panel, but I see no way to avoid it if the quarter is glued to the flat. This part of the manual needs more detail.
I’ll assemble my bottom today but wait for more feedback before gluing the quarter panels.