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John has played this slightly differently from show to show.  I'll try to cover all the different
ways he's played it, but it really comes down to how you think it sounds best.  There is no "right" way.

Mid-verse riff:

-22222222xx222222
-33333333xx333333 ...into the G chord
-2222222242222222
-0000000000000000
-----------------
-----------------

Intro:
D A Bm G (can be played once, twice, or not at all)

      D                              A
These roses are the pleasures of the flesh
      Bm                                      G
These ones here they are the pleasures of the spirit
    D                            A
And tucked behind a pornographic picture in a frame
    Bm                                      G
The troops found the pierced heart and they all gathered near it

D G D G (*mid-verse riff may be used for the D's)

        D                          A
And the dust clouds bloomed in the dark
        Bm                          G
And the face gazed up from the frame
D                             A
Roomful of French troops in a Franciscan abbey
D                             G
History does not recall their names

      (G)                      A            D
Of the several things that you have to do today
               G
You're gonna regret one
(G)             A              
This generation asks for a sign
D                 G
 It isn't gonna get one

D A D A (John has also played "D Asus4 D D" instead)

D                                    A
Berthe then took the pictures to the priest
        Bm                                    G
And the priest fell on his face and pawed the floor
        D                    A
And the story lived on for a decade or two
    Bm                        G
But no one really knows it anymore

D G D G (*mid-verse riff may be used for the D's)

        D                            A
But the blessed heart is seen in the airbrush
        Bm                              G
And the blessed heart is beating on the wind
        D                                 A
And the bodies of the faithful stacked by dozens by the roadsides
Bm                        G
Stripped and scourged and skinned

      (G)                      A            D
Of the several things that you have to do today
               G
You're gonna regret one
(G)             A              
This generation asks for a sign
D                 G
 It isn't gonna get one

D A D D (use Asus4 in place of A if you did earlier)

Thanks to Mike (green_vii) for helping out!