The clean verses are played with a moveable chord in this shape the whole time.
I watched a video of them recording in the studio to figure it out. i=index, m=middle, r=ring

e|-|r|
B|-|r|
G|-|r|
D|i|-|
A|-|m|
E|-|-|


-Intro-
e|----------------------------------------------------------------|
B|-----------------------------------------------7-(b9)7--7---------|
G|-(b9)8--9p8-/6---6---------------6-6-4-6-9p8-(b9)---------(b9)8h(b9)8-|
D|-------------(b9)--8-6--8----6/8----------------------------------|
A|----------------------------------------------------------------|
E|----------------------------------------------------------------|

-Verse 1 - clean-
For a lot of these clean parts, he's comping more than he is playing rhythm guitar, so the
progression and rhythm change up a lot while still following the same basic skeleton.

"Last call for alcohol..."
e|-6-7-|-6-7-(b9)|
B|-6-7-|-6-7-(b9)|
G|-6-7-|-6-7-(b9)|
D|-5-6-|-5-6-8-|
A|-6-7-|-6-7-(b9)|
E|-----|-------|

"I am Emperor Ronald Reagan..."
the rhythm locks down to the familiar California Uber Alles progression
e|-6-7---(b9)7-6-|-6-3-4-|
B|-6-7---(b9)7-6-|-6-3-4-|
G|-6-7---(b9)7-6-|-6-3-4-|
D|-5-6---8-6-5-|-5-2-3-|
A|-6-7---(b9)7-6-|-6-3-4-|
E|-------------|-------|

"now you're gonna pray in school"
e|-6--4--12-(b9)|
B|-6--4--12-(b9)|
G|-6--4--12-(b9)|
D|-5--3--11-8-|
A|-6--4--12-(b9)|
E|------------|

-Clean Chorus-
"California uber alles..."
e|-6-----6-----6--12-|
B|-6-----6-----6--12-|
G|-6-----6-----6--12-|
D|-5-----5-----5--11-|
A|-6-----6-----6--12-|
E|-------------------|

"(the do-opps)"
e|-6--4--12-(b9)|
B|-6--4--12-(b9)|
G|-6--4--12-(b9)|
D|-5--3--11-8-|
A|-6--4--12-(b9)|
E|------------|

-Verse 2 - distorted-
(just like normal version of C.U.A.)
"Klu Klux Klan will control you..."
e|------------|--------|
B|------------|--------|
G|-8--(b9)-11-(b9)|-8--6---|
D|-8--(b9)-11-(b9)|-8--6-4-|
A|-6--7--(b9)-7-|-6--4-4-|
E|------------|------2-|

-Distorted Chorus-
"California..."
e|---------------|----------|
B|---------------|----------|
G|-8---8----8----|-8--6-----|
D|-8---8----8--6-|-8--6-7-4-|
A|-6---6----6--6-|-6--4-7-4-|
E|-------------4-|------5-2-|

-Verse 3 - clean-
(1 measure instrumental) then "...ah yeah, that's it. Just relax..."
e|-6--4--12-(b9)|
B|-6--4--12-(b9)|
G|-6--4--12-(b9)|
D|-5--3--11-8-|
A|-6--4--12-(b9)|
E|------------|

-Bridge - distorted-
"Welcome to 1984..."
strum hard and occasionally only on the root note, palm mute, and add in the 3rd note
of the power chord as your ear sees fit.
e|----------------|
B|----------------|
G|(8)-(6)---------|
D|-8---6--(7)-(4)-|
A|-6---4---7---4--|
E|---------5---2--|

-Distorted Chorus-

-Outro- 
Strums in () mean it's a rest but keep that strum going
e|-----------------------------------------------------|---------|
B|-----------------------------------------------------|---------|
G|-8-------8-8-8-8-----8-8-8-6-----6-6-6-11----6-------|-8-8-8-8-|
D|-8-------8-8-8-8-----8-8-8-6-----6-6-6-11----6-------|-8-8-8-8-|
A|-6-------6-6-6-6-----6-6-6-4-----4-4-4-(b9)----4-------|-6-6-6-6-|
E|-----------------------------------------------------|---------|
   D(u d u)D U D U(d u)D U D U(d u)D U D U(d u)D(u d u)  D U D U 


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| /   slide up
| \   slide down
| h   hammer-on
| p   pull-off

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