My interpretation is going to be a bit different from what I'm reading here.
"I know a thing about contrition
Because I got enough to spare"
He isn't sorry for what he's done, and he doesn't actually put into effect the contrition that he should have.
"And I'll be granting your permission
Cause you haven't got a prayer"
Basically he's saying how there's no prayer that could save him, and he's telling people that he doesn't mind that.
"Well I said hey, hey hallelujah,
I'm gonna come on sing the praise.
And let the spirit come on through ya,
We got innocence for days!"
This is a mockery of the lengthy rituals that some people go through to cleanse themselves of sin (I'm Christian, but I don't see this as an insult to that religion, more to the religious freaks within it).
"Well, I think I'm gonna burn in hell,
Everybody burn the house right down."
He thinks he's going to hell so they might as well burn the house so he can get there faster and at the same time make his life a hell.
"And say, ha
What I wanna say
Tell me I'm an angel,
Take this to my grave.
Tell me I'm a bad man,
Kick me like a stray.
Tell me I'm an angel,
Take this to my grave."
So, he says that he, as The Patient, as he's lying there pretty much dying, people call him an angel for enduring that, but they don't know what he's done (hence Mama's war theme, so they can take that to his grave because in actuality it isn't true. He'd rather them treat him like he deserves to be treated.
"S-I-N, I S-I-N"
He may be lying there unable to go and do anything, but there's still all the memories and thoughts of Sin.
"You play ring around the ambulance,
Well like you never gave a care."
He's saying how if you flirt with death like he did...
"So get the choir boys around you,
It's a compliment, I swear."
....they're going to try to save you, convert you, and it's awfully annoying but everyone sees it as a compliment (the second line is thus sarcasm).
"And I said, ashes to ashes, we all fall down,
I wanna hear you sing the praise,
I said, ashes to ashes, we all fall down,
We got innocence for days!"
He's saying that we're all going to die, and that he's going to die, and he finds it amusing how people make a bigger deal out of religion than is needed.
"You better run like the devil,
'Cause they're never gonna leave you alone!
You better hide up in the alley,
'Cause they're never gonna find you a home!"
So run away from those people lest they never stop pestering you, and settle with the fact that you'll never fit in anywhere.
"And as the blood runs down the walls,
You see me creepin' up these halls.
I've been a bad motherfucker
Tell your sister I'm another
Go! Go! Go!"
This could mean that he killed someone and lied about his past so that he could get close to someone's sister.
~This may or may not be accurate, but when I lip sync it in the dark in a closet some nights, this is what I imagine!~
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