The 12 string guitar continues through the verses as well as the intro. When you listen to the above MP3 example you can hear up to 7 guitars playing at once. Playing this in a standard band would make this a difficult song to add to the repertoire. That's why you don't see too many bands play it (or play it well).
This muted guitar plays through both verses, it has no note or tone value, it is purely percussive.
Bass Riff
This guitar part is played in verse 1 & 2, this riff re-enforces the bass line, giving the bass a punchy dominant sound. It is subtle in the mix and you could almost think that it's not even there. This is a good example of how song parts and instrument blend to create a bigger picture.
Listen to the 16 bars below (Left: 12 string Right: Muted Bass)
Harmony Riff 1
These are two electric distorted guitars harmonising through the 2nd half of the 1st & 2nd Verse. You can't play both these parts together on the one guitar and get the same sound. They have to be played by two guitarists going through two separate amps.
Listen to the 9 bars below (Left: Guitar 1 Right: Guitar 2)
Harmony Riff 2
This riff is similar to the one above. To get more sustain out of your notes try using a vibrato.
Listen to the 8 bars below (Left: Guitar 1 Right: Guitar 2)
The next riff uses harmony notes again. A simple way to explain harmony notes is that it's the same riff but played either higher or lower than the main riff. There is a lot more to it than that of course, you have to know the key of the songs/solo and use either a 3rd or 5th above as a standard.
Listen to the 8 bars below (Left: Guitar 1 Right: Guitar 2)