without a doubt this song is about the speaker's gripe with faith/religion.
he's tormented: he beleives one thing, lives for "you," i.e. God; yet at the same time hes betraying his faith w/ his actions

"What junkie says is not what junkie do,
But it's all for you
And the tricks he turns will always shine right through,
But it's all for you."

Another drugs / religion metaphor and all the while, we aren't focused on the real deal: the people that love us.

A junkie continues to use even through his own religious beliefs, denying the adverse effect of his addiction. He convinces himself that "it's all for you", that it's all for the betterment of his life, his connection with God. He hurts those around him with his lies and denial, while he loses his connection with the things he treasures most in life.

I see this song as told from the perspective of a fundamentalist preacher--most likely a fundamentalist Christian who preaches to born-agains.

-In goodness wake I'll always say I do,
-That it's all for you

Everything good I've done, it is for God (or Jesus, or Allah).

-And tricks I'd turn would always shine right through,
-But it's all for you.

Though I lie through my teeth ("tricks I turn"), and that's how most people see me, God knows I am devout and I'm doing it for the right reason.

--Like a stream overflowing
--Unpredictable
--A new confidence like a new king.

I have the ultimate confidence in my charms, in the strength of my faith. It gives me power, "like a new king," and that only swells my confidence. The faith of my subjects overflows and what they may do is unpredictable.

-Like a breeze levitating
-To raise a sunken soul
-And to the surface shines like a new pin.

We are all raised spiritual through belief in Christ. Even the worst man ("Sunken soul") can be raised to heaven, and can shine with Goodness.

-Like a dream synchronising
-With the one I missed the most
-A concentrated love from a new queen.

In heaven we can meet with those we miss the most.

-Like a wave stabilising
-I walk a tighter rope
-And my new victim shines like a new pin.

The rope of virtues is tougher to walk as fame grows, but every sinner I touch I make shine with Virtue.

-I can feel lies within the
-Gospels that I'm sold
-The tactless sentiments are a new pain.

But I know that I am overzealous, that I am greedy, and that I am a bad man at heart. The Gospels say I'm a devil.