Just quickly roughed it out since its getting late, will try and update it when I can, 
when it changes to the verse I didnt really pay much attention to the second guitar, just 
with the muting and listen to when the vocals come in and you can get it.

Tuning: Standard - seems to be

Intro A:

Gtr I
e|--------------------------|
B|----------------------1-3-|
G|--------------------3-----|
D|---2p0-3p0---2-p0---------|x4
A|-----------1------0-------|
E|-3------------------------|

Or I think I recall that josh moves up the fretboard when playing the riff so in that 
it could be this, personally I prefer the above.
e|--------------------------|
B|--------------------------|
G|----------------------5-7-|
D|--------------------8-----|
A|---7p5-8p5---7p5----------|
E|-3---------6-----5--------|

Intro B:

Gtr I
e|--------------------------|
B|----------------------1-3-|
G|--------------------3-----|
D|---2p0-3p0---2-p0---------|x4
A|-----------1------0-------|
E|-3------------------------|

GtrII
e|--------------------------|
B|--------------------------|
G|--------------------------|
D|--------------------------|x4
A|-5-5-5-5-5-5--------------|
E|-3-3-3-3-3-3--------------|

Intro C:

Gtr I
e|--------------------------|
B|----------------------1-3-|
G|--------------------3-----|
D|---2p0-3p0---2-p0---------|x4
A|-----------1------0-------|
E|-3------------------------|

GtrII
e|--------------------------|
B|--------------------------|
G|--------------------------|
D|--------------------------|x4
A|-5-5-5--------------------|
E|-3-3-3--------------------|

Intro D:

Gtr I & II
e|-------------------------|
B|-------------------------|
G|-------------------------|
D|-----2p0-3p0---0-0-------|x2
A|-------------0-----3p0---|
E|-3-3-------------------3-|

Intro E:

Gtr I & II
e|-----------|
B|-----------|
G|-----------|
D|-0-0-------|
A|-----3p0---|
E|---------3-|

Intro F:

Gtr I & II
e|-------------------|
B|-------------------|
G|-------------------|
D|-------------------|
A|-5-5--5-5--5-5-5-5-|
E|-3-3--3-3--3-3-3-3-|

Intro G:

Gtr I & II
e|-------------------------|
B|-------------------------|
G|-------------------------|
D|-----2p0-3p0---0-0-------|x2
A|-------------0-----3p0---|
E|-3-3-------------------3-|

Intro H:

Gtr I & II
e|-----------|
B|-----------|
G|-----------|
D|-0-0-------|
A|-----3p0---|
E|---------3-|

Intro I:

Gtr I & II
e|-------------------|
B|-------------------|
G|-------------------|
D|-------------------|
A|-5-5--5-5--5-5-5-5-|
E|-3-3--3-3--3-3-3-3-|

Intro J:

Gtr I
e|--------------------------|
B|----------------------1-3-|
G|--------------------3-----|
D|---2p0-3p0---2-p0---------|x4
A|-----------1------0-------|
E|-3------------------------|

GtrII
e|--------------------------|
B|--------------------------|
G|--------------------------|
D|--------------------------|x4
A|-5-5-5-5-5-5--------------|
E|-3-3-3-3-3-3--------------|

Intro K:

Gtr I
e|----------------|
B|---------1-3/18-|
G|-------3--------|x8
D|----------------|
A|----------------|
E|----------------|

Gtr II
e|----------------|
B|----------------|
G|----------------|
D|----------------|x8
A|-5-5-5----------|
E|-3-3-3----------|

Verse A:

Gtr I
e|----------------------|
B|-3---6----8-----11----|
G|-5b7-8b10-10b12-13b15-|
D|----------------------|x3
A|----------------------|
E|----------------------|

e|--------------------------------------|
B|-3---6----8------6----6h8--6---6------|
G|-5b7-8b10-10b12--8b10--------7---7-\6-|
D|--------------------------------------|
A|--------------------------------------|
E|--------------------------------------|

Gtr II
e|-------------------|
B|-------------------|
G|-------------------|
D|-------------------|
A|-5-x-8-xx10~-13--x-|
E|-3-x-6-xx8~--11--x-|

e|------------------|
B|------------------|
G|------------------|
D|------------------|
A|-5-x-8-xx10~-8--x-|
E|-3-x-6-xx8~--6--x-|