A beautiful and haunting song I have played a thousand times. I think the posted lyrics are good but I do interpret and guess a few words differently as follows:

In a dark winter Tokyo
In the Mahjong water he wades
Severed pasts drumming through his hands
Though he comes to the water ways

In the hallways they're lying there
In the red blossom of the day
In your arms there is nothing left
Though he comes to the water ways

My whole life
Is the mystery
That I can't take

Oh wings
That are Calvary
Upon this day

I would love to heal you now

In a dark winter Tokyo
In the Mahjong waters they wade
Severed pasts sweeping through their hands
Though he comes to them on the way

In the arm of the young
Red blossom of the day

All I wanted to see
Is that I am better
All I want to believe
Is that I am better
From here on
All I wanted to see
Is that I am better
From here on

i am pretty sure your lyrics are wrong.
by a lot.

i get "mahjong waters"
i get "mystery that i can't bear"

the rest i can't make out.
but i don't hear what you put.

NOTES: see http://www.youtube.com/watch?v=aNi_a5CUybs for a live version to compare against.
i was using high quality headphones, so i'm confident with most of the lyrics.
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in a dark winter tokyo
in the Mahjong parlour he waits
severed past throbbing through his hands
nobody comes to the one who waits
in the hallways they're lying there in the red blossom of the gaze
in your arms there is nothing left
we are all on the wait

my whole life is a mystery that i can't break
our lings and Calvary of our mistakes
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NOTES: the 'L' is before the 'V' when she sings. see http://en.wikipedia.org/wiki/Calvary. i have no idea what the first words of that line are though. it's not "oh". more like our/are and there is an 'L' sound that follows. it's possibly another place name that i am unfamiliar with.]
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i would love to heal you now

in a dark winter tokyo
in the Mahjong parlours they wait
severed past sweeping through their hands
nobody comes to the ones that wait

in the heart of the young they gloss over the pain

all i wanted to see is that i am better
all i want to believe is that i am better
round and round
all i want you to see is that i am better
round and round

Although I'm stumped on quite a few lines, I'm fairly sure it's 'In the Mahjong parlor he waits/Severed pasts thrumming through his hands/...comes to...on their way

My whole life
Is a mystery
That I can't bear

Day sounds like 'stays', although most of that verse is garbled.

In the hour of the young/There dawns...

All I want you to see/is that I am there/All I want to believe/is that I am there

I'm playing this by ear just as much as anyone else, though, so please feel free to disagree with me. Anyone else want to take a crack at it?

it kind of sounds like "cavalry" instead of "camery"