For the "E" chord play this:
eb|-0-|
Bb|-0-|
Gb|-x-|
Db|-2-|
Ab|-2-|
Eb|-0-|

It doesn't sound a whole lot different but on an acoustic it makes a difference.

I'm not completely sure of the F# in the intro but there is a chord change and it sounds 
about right.
The intro progression is repeated at the end of the first chorus as well.

Intro
E G Am C G F# G

Verse 1:
G
Dead star shine
Badd9
Light up the sky
    Am
I'm all out of breath
   C
My walls are closing in

G
Days go by
Badd9
Give me a sign
     Am
Come back to the end
    C
The shepherd of the damned


Chorus:
E              D        C
I can feel you falling away
   G
No longer the lost
   D
No longer the same
    E             D             C
And I can see you starting to break
     G
I'll keep you alive
       D
If you show me the way
   E        D
Forever and ever
    G            C
The scars will remain
    G
I'm falling apart
D                            E   G Am C G
F# G
Leave me here forever in the dark


Verse 2:
G
Daylight dies
Badd9
Black out the sky
     Am
Does anyone care?
   C
Is anybody there?

G
Take this life
Badd9
Empty inside
    Am
I'm already dead
     C
I'll rise to fall again


Chorus:
E              D        C
I can feel you falling away
   G
No longer the lost
   D
No longer the same
    E             D             C
And I can see you starting to break
     G
I'll keep you alive
       D
If you show me the way
   E        D
Forever and ever
    G            C
The scars will remain
    G
I'm falling apart
D                            E
Leave me here forever in the dark


Bridge:
D   G                 D E
God help me I've come undone
G          D            C
Out of the light of the sun
D   G                 D E
God help me I've come undone
G          D            C
Out of the light of the sun


Chorus:
E              D        C
I can feel you falling away
   G
No longer the lost
   D
No longer the same
    E             D             C
And I can see you starting to break
     G
I'll keep you alive
       D
If you show me the way
   E        D
Forever and ever
    G            C
The scars will remain


Outro: (palm mute the first time around)
G              D
Give me a sign
D
There's something buried in the words
E              C
Give me a sign
C
Your tears are adding to the flood

     G              D
Just give me a sign
D
There's something buried in the words
E              C
Give me a sign
C
Your tears are adding to the flood

     G              D
Just give me a sign
D
There's something buried in the words
E              C
Give me a sign
C
Your tears are adding to the flood


   E        D
Forever and ever
    G            C
The scars will remain