[link to original on tumblr]
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I listened to the third disc of The Pet Sounds Sessions this morning (about which I'll have more posts later), and I realized that "Sloop John B" has a similar structure, just with flutes instead. In the later choruses of "Sloop John B," there's a flute phrase and then about two measures of rests before an-other flute phrase. That same pattern is here: guitar phrase, two measures of rests, and then an-other guitar phrase.
When I was recording this though, I discovered that the first two phrases don't follow that structure. There's the first phrase, then three measures of rests, and then the second phrase. I'm pretty sure that's a deliberate departure since the line immediately before that phrase is "You needed my love, and I know that I left at the wrong time." There's a wrong time in the music and in the lyrics.