I probably noticed this even the first time I listened to the song, but the line "Our Father, who art in heaven" at the beginning of the alternate version of "Heaven Only Knows" is taken from the Lord's Prayer (Matthew 6:9).
"Away" in the lines "If you could turn night into day / I could stop it slippin' away" is sung with a melisma (F# F# E) for a sense of (metaphorical) movement.
