system
Given the following post, respond as if you're commenting on Reddit:
human
[WH40K] What goes on during the Soul-Binding process and why is it so painful? Don't they have anesthesia?

In fact, what is a soul anyways and how can it feel pain in the Warp?
gpt
Ok... First, what is a soul? In 40k (this is pieced together from numerous novels and codex) a soul is the conduit between the physical body and the Warp. Everything physical reflects in the Warp, but only living things seem to generate a natural connection. This connection links the Animus (the body) with the Anima (it's emotional response and echo) and serves as a two-way conduit for emotion and warp-energy. The stronger the connection, the 'wider' the channel, and the more powerful the soul. 

Over time, this channel seems to absorb memories, emotions and most importantly the raw power of the Warp, forming a micro-entity in and of its self. The more powerful the soul, the faster this happens, with the Eldar seeming to be the most rapidly developing... After a point, this collection of energy and memories develops its own consciousness, based on the living entity it is attached to. 

While connected, there is a degree of protection. Warp-predators cannot break the connection from their side, and are thus unable to really affect the Soul so long as its body remains connected. They can, however, use a sufficiently powerful soul as a conduit TO the physicall world, where they can wreak untold havoc, including killing the body.

Upon death, the collected energy and memories of the soul flow into the Warp, in most cases as barely a flicker. Humans lack the strength to maintain and semblance of consciousness after death, and most psykers are only able to experience dull echos. Powerful Psykers and the Eldar, are strong enough to 'remain' entirely aware in the Warp, and their relative power causes their 'release' to blast off like a meteor, attracting every predator around. While a soul cannot technically feel pain, it does usually have the memory of it, and such powerful souls are fully aware as they are picked appart by the denizens of the Warp.

Now... The Emperor is a strange bird.. he is, in essence, an immensely powerful Daemon in the physical universe, a warp-entity inhabiting a carefully attuned shell, similar to the Eldar Avatars of Khaine, though more whole.The Soul Binding is, essentially, posession, part of the Emperor's immense warp-presence entering the host and 'claiming' it. Once claimed, other Daemons have a far harder time posessing someone. 

The pain and physical damage (usually having the eyes burned from their skulls) likely comes from the fact that the Emperor is PHYSICAL. He is entering the soul through the physical side, the side that feels pain. Even a mote of his power (full posession would obliterate the host's body) can cause immense damage to an inappropriate host, and as we all know, damage is usually accompanied by pain.