[link to original on tumblr]
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I'm pretty sure that it's just a descending chromatic phrase (D, C#, C), but that final C is sort of dissonant because it's above a G major chord (G, B, D).
I recorded this with electric guitar and reed organ. I didn't feel like setting up a microphone to record acoustic guitar, and my voice is too low for it to have sounded good if I sang it.
To some degree, the harmony part here is a precedent to that in "Maybe after He's Gone," where there are chromatic phrases in both harmony parts during the choruses (Rod's part is E, D#, D, C#; Chris' is A, F#, F, E).
Come to think of it, there's a harmony part like this in "She's Not There" too. I'm pretty sure that the "(too) late to say you're sorry" is sung to F#, F, E.