Hero (film)/WMG

WARNING: Unmarked spoilers and wild mass guessing for the webcomic HERO. Read on at risk of ridiculousness and spoilage.

The first one and a half acts never happened
All that stuff with the witch and the priest and the cat and the wolf? It was all part of the dream-state of the narrator's formation period, when Valentine was making him. It explains why D'Urfe and the rest never came after him before, why his memories of his time with the witch seemed to fade, and why Valentine was a door.
 * His journey down the hill and into the watchtower was representative of his nearing completion, gradually drawing out of the dream-state.
 * The door shattering and turning into Valentine? That was the point where he actually entered physical reality.
 * The witch is based on residual Eira-memories of Vin, the priest on memories of the tiger-voiced man, and the cat on memories of Valentine.
 * Also supported in "a space between cities", where the narrator himself questions the reality of his stay in the witch's house.

The colorful egg will contain a heart
For whom, it is not certain, but all this stuff about people -- demons, presumably -- locking up their hearts to become invincible puts one in mind of Koschei, whose soul is hidden inside an egg (which is then hidden under many layers of deception and so forth). Perhaps it will come in handy at the end to free or defeat a heart-less demon.

Juno and Ganymar were each other's former spouses when they were human, and also Eira's parents.
Golems appear to have a predetermined amount of knowledge when they are created. The narrator knows how to read, write, walk, and talk, for instance--it simply takes him a little longer to catch on to subtleties like using "the duck" to refer to a motorcycle.

The exact amount of time between Eira's birth, his parents' deaths, and the creation of Ganymar and Juno is never specified. When D'Urfe tells Juno of how he was asked to take care of Eira, she says that it sounds like a story she knows. The phrase "It is an old story", when used by D'Urfe, does not seem to refer to how long ago it actually happened--Eira was clearly a few weeks old at the most, and Juno had only just heard it--but to the cyclic nature of history.

And then there's the genuine affection Ganymar and Juno show towards Eira, despite initially being superpowered babysitters--see Juno's meeting of Valentine, where Valentine says that her job is not specifically to kill demons but to keep watch over Eira, yet she kills demons anyway if they even get close to him. Ganymar also intentionally tracks Valentine down to fight over Eira, and collapses into tears whenever Eira's death comes up.

It would, however, make Eira's death even more tragic.

The narrator gained a soul when he decided to pet the cat in the City of Delight.
Conveniently, he reached it just after leaving Ganymar and Juno, but before he met D'Urfe. Valentine told the narrator not to pet the cat. But the narrator did anyway, which exhibits free will. Therefore, he got a soul. Possibly the cat even remembered Eira, and gave the narrator one of its nine lives.

The children who warned Valentine in "a space between cities" were two halves of the Serpent.
The Serpent's transformation abilities appear to be limited to children's forms, especially when he is not at full power--as demonstrated when the narrator causes snowfall in "the winter meadows", and just before Venice disappears.

They are both polite and redheaded, and Valentine recognizes them as being his relations. For whatever reason, the Serpent was split in two, resulting in two forms. He simply recovered before gathering a battalion for his entrance in "cloud country".