This phrase is used here to mark the beginning of a new part of the story. If your language has a way for doing this, you could consider using it here. Alternate translation: "It happened that"
The phrase "which he had made" tells about the window. Some languages may need to make this phrase a separate sentence: "Noah had made a window in the boat. It came about after forty days that he opened the window" (See: [[rc://en/ta/man/jit/figs-distinguish]])