1) He's a little out of tune during the clean intro. You never notice it in the track but it's a lot more exposed when isolated.
2) The song is performed in a Drop D tuning, which means that the low E string is detuned to D.
3) The most distinctive thing about the guitar track is the Leslie speaker effect used during the verse. A Leslie speaker, mostly used with organs (a Hammond B-3 and a Leslie model 122 is the classic combination), has a rotating treble horn and rotating drum around the low frequency speaker. It's been used with a guitar since the 60's, most famously in The Beatles "While My Guitar Gently Weeps." The Leslie has a slow and fast speed, with Black Hole Sun using the fast speed and recorded in stereo.
4) The distorted guitar in the chorus is also recorded in stereo, as is the wah guitar solo (which Guitar World magazine ranked #63 among the top 100 guitar solos) and outro.
5) Listen to the noises at the end of each part before the next part kicks in. These would certainly be cleaned up if recorded today.
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