Okay, I've been totally obsessed with this show. A couple of things I recently realized/discovered while poking around on the internets:
a) Half of the fucking cast is from Deadwood (sans funny facial hair). I knew they looked familiar.
b) I'm revising my initial theory on John's origin. I no longer think he's the messiah - I'm pretty sure that he's God.
I knew that John's last name (Monad) seemed familiar, so I hit Wikipedia for some answers this is what I found:
Monad (apophatic theology)
In many Gnostic systems (and heresiologies), God is known as the Monad, the One, The Absolute, Aion teleos (The Perfect Æon), Bythos (Depth or Profundity, Βυθος), Proarkhe (Before the Beginning, προαρχη), and E Arkhe (The Beginning, η αρχη). God is the high source of the pleroma, the region of light. The various emanations of God are called æons.
Within certain variations of Gnosticism, especially those inspired by Monoimus, the Monad was the highest God which created lesser gods, or elements (similar to æons).
According to Hippolytus, this view was inspired by the Pythagoreans, who called the first thing that came into existence the Monad, which begat the dyad, which begat the numbers, which begat the point, begetting lines, etc. This was also clarified in the writings of Plato, Aristotle and Plotinus. This teaching being largely Neopythagorean via Numenius as well.
This Monad is the spiritual source of everything which emanates the pleroma, and could be contrasted to the dark Demiurge (Yaldabaoth) that controls matter.
The Sethian cosmogony as most famously contained in the Apocryphon ('Secret book') of John describes an unknown God, very similar to the orthodox apophatic theology, although very different from the orthodox credal teachings that there is one such god who is identified also as creator of heaven and earth. In describing the nature of a creator god associated with Biblical texts, orthodox theologians often attempt to define God through a series of explicit positive statements, themselves universal but in the divine taken to their superlative degrees: he is omniscient, omnipotent and truly benevolent. The Sethian conception of the most hidden transcendent God is, by contrast, defined through negative theology: he is immovable, invisible, intangible, ineffable; commonly, 'he' is seen as being hermaphroditic, a potent symbol for being, as it were, 'all-containing'. In the Apocryphon of John, this god is good in that it bestows goodness. After the apophatic statements, the process of the Divine in action are used to describe the effect of such a god.
Plus, The symbol that he keeps tracing with his foot looks like the Monad symbol with a line connecting the perimeter to the radius.