My interpretation of the record is that of Death and the assimilation of two or more aspects of personality. Specifically one aspect, Rael, appears to not accept death while Brother John appears to be embracing of it. I tend to look at the first five songs relating to actual life and some event that takes Rael's life or leaves him comatose. The Lamb being a picture of his life, with Fly being the seeing of the white light. Broadway Melody is some sort of picture of his life or the wants in his life. Finally Cocoon and Cage talking of the divide between the physical and spiritual.
The Grand Parade is strange but seems to be taking place in a spiritual limbo that is not life or death. He is walking past the ready bodies of the unborn which seem to be awaiting spirits and sees that they are sometimes people he knows, as if there is a limited supply of variation. That may also be a reference to reincarnation but I have not though long enough on that issue to come to any conclusion. Back in New York City is Rael trying to live struggling to hang onto the life, as I see it.
Hairless Heart has seems to have two currents going through it. The connections of his life holding him and sexuality. The shaving part seems to refer to cutting the connections to his heart and moving on a bit. The sexuality comes back with the next song Counting out time. It seems to be almost a lament of death as he never got this part right in life. This subject comes back later.
Carpet Crawlers and Chamber are hard to dig through but I feel they are talking about his confusion of spirit and not understanding. There are aspects of life and its confusion here too, who you take advice from and how you life. Lily white Lilith appears to be part of this spiritual second as well, she may represent some aspect of Rael as well a stunted intuition or spiritual aspect he finds that guides him to the next part.
Anyway and Anaesthetist pretty clearly have to deal with Death. I think this is death finally taking him from his physical death that happened in Fly. That is why the "Sorry to keep you waiting" line seems to be there. This meeting with Death dives him onto the next section the afterlife it appears as he starts resolving aspects of himself in the last few sections.
In Lamia and Slippermen the concept of sexuality returns. It seems to be some sort of negative and destroying force within Rael his sexuality and youthful drives. The Slippermen shows the negativity of it and he removes or resolves it. You will note John is there in this part seeming to be something that is shared across both of the two aspects of Rael/John. But later you see Rael trying to reclaim this component of himself chasing after the tube. John is uninterested in this idea and moves on.
We finally are left with the Rapids and It. Water is often linked with emotion in dreams, the water seems to be emotion of death and want fighting with Rael he finally catches John and the two are joined in It. With Johns face being his own. It finally tells of the movement of spirit between the two and the final assimilation and ascension of spirit to the greater states. I personally would say moving on to heaven but I am unsure of Gabriele's relationship with Christianity.
One last area of debate is the narrator. In my opinion there are three narrators, at least, who lend their voices to the story. Those are Rael, Brother John, and a omnipresent third who I assume is God. The Lamb Lies down and It both appear to have this third voice.