I believe that the song refers to a religious experience as already mentioned, but it is also an admonition to others to search out what they beleive.

"I skimmed across black water, without once submerging
Onto the banks of an urban morning"

This perhaps coming from the first person perspective of Jesus Christ or of Peter who both walked on water, or again a religious experience of the poets own view.

"That hungers the first light, much much more than the mountains ever do."

The hunger perhaps being the desire of humans to figure everything out including God, and attempting to "rationalize" thier religion

"And she like a ghost beside me, goes down with the case of a dolphin
And emerges unlearned, unshamed, unharmed
For she is perfect creature, natural in every feature"

The she here could be refering to the mountains mentioned previously or to something else, that does not desire to search out her religion and merely accepts it by faith.

"And I am the greek(geek?) with the alchemists' stone."

This again refering to the one who seeks everything out as a geek would, or a suppose a greek would depending on the era.

"For all of you who must discover,
For all who seek to understand,"

The poet is now speaking to those that want to discover God, those that are looking for God.

"For having left the path of others
You'll find a very special hand."

You will find him, by departing from those that blindly follow their faith, and searching out what you belive, you will find "a very special hand" perhaps a reference to the hand of God.

"And it is a holy thing, and it is a precious time
And it is the only way"

Holy thing and precious time are self explanatory in the light of the hand of God. And perhaps a religious reference here to Jesus being the Way?

"Forget-me-nots among the snow, it's always been and so it goes"

This part I have no idea about???

"To ponder his death and his life eternally"

Pondering Jesus' death, and his eternal life (post resurrection)

"One bright blue rose outlives all those
two thousand years, and still it goes
to ponder his death and his life eternally"

The bright blue rose, perhaps refering to Christianity, or to Jesus Christ, irregardless it has existed for 2000 years, and again a reference to pondering Jesus.


Thats my interpretation. Do with it what you will