A lot has changed since original post. Hull got properly sanded AND shaped, with stern lowered. Gaps filled with white polystyrene (0.5 mm sheets), then putty and sanded.
Upper deck gun ports will be closed, so I have glued in squares of plastic to be able to put gunport covers later on.
Now- of course that mini- lower deck in bow section should be on same level as entire deck along the ship, but since "interior" will not be visible, I was not correcting those mistakes. Today I've prepared drawings of deck for laser cutting/ engraving. Proper grettings, as well as correct (more or less) plank layout.