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OK, so there really aren't that many mentions of windows in the poem, but it does make us think of how Ginsberg got kicked out of school for writing obscenities on the windows of his dorm room. In poetry in general, windows are a classic metaphor for the eyes.
Line 7: Ginsberg was suspended from Columbia University for writing obscenities on the windows of his dorm room. However, the "windows of the skulls" sounds like a metaphor for the eyes.
Line 84: And, sure enough, here windows are a metaphor for the eyes of Moloch.